From 9fce2df8f4cdab1f82651ed041084c19cace6818 Mon Sep 17 00:00:00 2001 From: Danielle WELTER Date: Wed, 9 Sep 2020 22:09:57 +0200 Subject: [PATCH] Fixed makefile so it doesn't delete all the build products --- Makefile | 4 +- build/curatO-edit.owl | 2413 ------- build/curatO-merged-with-imports.owl | 9634 ------------------------- build/curatO-reasoned.owl | 9632 ------------------------- build/curatO.owl | 9647 -------------------------- 5 files changed, 2 insertions(+), 31328 deletions(-) delete mode 100644 build/curatO-edit.owl delete mode 100644 build/curatO-merged-with-imports.owl delete mode 100644 build/curatO-reasoned.owl delete mode 100644 build/curatO.owl diff --git a/Makefile b/Makefile index ae9c32a..899ad1f 100644 --- a/Makefile +++ b/Makefile @@ -64,7 +64,7 @@ build/bfo-iao: | build clean: | release @echo "Removing build files" && \ - rm -rf build + rm -rf build/*.owl # =============================== # CURATO TASKS @@ -116,7 +116,7 @@ build/annotate: build/robot.jar build --version-iri "$(OBO)/curatO/$(TODAY)/curatO.owl" \ --annotation owl:versionInfo "$(TODAY)" \ --annotation-file src/annotations.ttl \ - --output ./build/curatO.owl + --output curatO.owl # --output ./build/$(TODAY)/curatO.owl release: build/template build/merge build/reason build/annotate diff --git a/build/curatO-edit.owl b/build/curatO-edit.owl deleted file mode 100644 index 8082dc8..0000000 --- a/build/curatO-edit.owl +++ /dev/null @@ -1,2413 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Process - - - - - - - - - - - - - - - quality - - - - - - - - - - - - - - - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957282 - role - - - - - - - - - - - - - - - material entity - - - - - - - - - - - - - - - software - - - - - - - - - information content entity - - - - - - - - - Philippe Rocca-Serra - rule - - - - - - - - - - - - - - - measurement datum - - - - - - - - - Philippe Rocca-Serra - textual entity - - - - - - - - - - - - - - - - - - - - - Philippe Rocca-Serra - organization - - - - - - - - - data transformation - - - - - - - - - Philippe Rocca-Serra - recall - - - - - - - - - Philippe Rocca-Serra - F-measure - - - - - - - - - Philippe Rocca-Serra - precision - - - - - - - - - Natural language processing (NLP) is a process concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Natural_language_processing - natural language processing - - - - - - - - - text mining is the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Text_mining - text mining - novartis:text processing - - - - - - - - - sentence extraction is a technique used for automatic summarization of a text. In this shallow approach, statistical heuristics are used to identify the most salient sentences of a text. Sentence extraction is a low-cost approach compared to more knowledge-intensive deeper approaches which require additional knowledge bases such as ontologies or linguistic knowledge. In short "sentence extraction" works as a filter which allows only important sentences to pass. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Sentence_extraction - sentence extraction - - - - - - - - - string tokenization is the process of demarcating and possibly classifying sections of a string of input characters. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Lexical_analysis#Tokenization - string tokenization - - - - - - - - - the process of identifying an entity and marking it up from a free text input - Philippe Rocca-Serra - FAIRplus - concept recognition - - - - - - - - - Named-entity recognition (NER) (also known as entity identification, entity chunking and entity extraction) is a subtask of information extraction that seeks to locate and classify named entity mentions in unstructured text into pre-defined categories such as the person names, organizations, locations, medical codes, time expressions, quantities, monetary values, percentages, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Named-entity_recognition - entity name recognition - - - - - - - - - part-of-speech tagging (POS tagging or PoS tagging or POST), also called grammatical tagging or word-category disambiguation, is the process of marking up a word in a text (corpus) as corresponding to a particular part of speech,[1] based on both its definition and its context‚Äîi.e., its relationship with adjacent and related words in a phrase, sentence, or paragraph. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Part-of-speech_tagging - part of speech tagging - - - - - - - - - Philippe Rocca-Serra - string matching - - - - - - - - - Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_extraction - information extraction - - - - - - - - - Information management (IM) concerns a cycle of organizational activity: the acquisition of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposition through archiving or deletion. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_management - information management - - - - - - - - - the process of handling (from developing to maintaining and serving) controled vocabularies - Philippe Rocca-Serra - terminology management - - - - - - - - - the process of loading, serving controlled vocabularies and terminologies for access, browsing and selection - Philippe Rocca-Serra - terminology hosting - - - - - - - - - the process of searching a terminology with an input string for matching concepts - Philippe Rocca-Serra - terminology lookup - - - - - - - - - the process of handling (from developing to maintaining and serving) a formal knowledge representation, semantic artefact - Philippe Rocca-Serra - ontology management - - - - - - - - - the process of searching an ontology with an input string for matching concepts - Philippe Rocca-Serra - ontology lookup - - - - - - - - - the process of marking up free text element (tokens, possibly resulting from tokenization) with a controlled term from a semantic artefact - Philippe Rocca-Serra - semantic tagging - semantic markup - - - - - - - - - a search process which relies on ontology to improve retrieval (e.g. query expansion) - Philippe Rocca-Serra - semantic search - - - - - - - - - the process of creating, assembling a formal semantic representation - Philippe Rocca-Serra - ontology development - - - - - - - - - the process of keeping a semantic representation up to date and in keeping with advances in the domain. This covers dealing with term submission, term obsoletion, release and evolution - Philippe Rocca-Serra - ontology maintenance - - - - - - - - - the process of re-arranging, re-engineering a formal semantic representation for optimization purpose, such as promotion of module reuse. - Philippe Rocca-Serra - ontology refactoring - - - - - - - - - the process of creating a formal semantic model from sets of existing modules extracted from other compatible semantic frameworks - Philippe Rocca-Serra - ontology composition - - - - - - - - - the process of augmenting a formal semantic model following batch submission of terms from a domain or modeling of a new domain of knowledge connex to the main them of the ontology - Philippe Rocca-Serra - ontology extension - - - - - - - - - an ontology extension process which happens on the fly, as users come up with the need. This is hard to accomplish as allowing user defined terms at will may lead to inconsistency and breakage. - Philippe Rocca-Serra - ontology dynamic extension - - - - - - - - - the process of formally describing a domain of knowledge - Philippe Rocca-Serra - knowledge representation - - - - - - - - - the process of breaking down a domain of knowledge according to rules - Philippe Rocca-Serra - knowledge formalization - - - - - - - - - the process of representing knowledge using formal rules, known as axiomsm, which allow automatic reasoning and solving - Philippe Rocca-Serra - axiomatic representation - - - - - - - - - the process of developing a domain representation by analysing data. - Philippe Rocca-Serra - data modeling - - - - - - - - - a data model is an information content entity which denotes and describes a domain of knowledge - Philippe Rocca-Serra - data model - - - - - - - - - the process of involving statistical methods, machine learning procedure to build a model which can be used to analysis new datasets and draw conclusions from never seen before data. - Philippe Rocca-Serra - model training - - - - - - - - - the process of classification is the process of identifying to which of a set of categories (sub-populations) a new observation belongs, on the basis of a training set of data containing observations (or instances) whose category membership is known - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/String-searching_algorithm - classification - - - - - - - - - data imputation is the process of replacing missing data with substituted values. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Imputation_(statistics) - data imputation - - - - - - - - - dealing with missing value is a process which aims to address the problems that occur when no data value is stored for the variable in an observation. Missing data are a common occurrence and can have a significant effect on the conclusions that can be drawn from the data. - Philippe Rocca-Serra - dealing with missing value - - - - - - - - - extract, transform, load (ETL) is the general procedure of copying data from one or more sources into a destination system which represents the data differently from the source(s) or in a different context than the source(s). - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Extract,_transform,_load - extract transform load process - - - - - - - - - the process of verifying that a data item supplied matches the specifications it is meant to comply with (e.g. an integer, a string,....) - Philippe Rocca-Serra - data type checking - - - - - - - - - the process of removing redundant entries which add volume without adding value - Philippe Rocca-Serra - duplicate removal - - - - - - - - - Philippe Rocca-Serra - pass through loading - - - - - - - - - the process of assessing the presence of a data item in a existing data strucuture or data storage system - Philippe Rocca-Serra - data lookup - - - - - - - - - the process of changing the encoding of information from one repertoir of characters convention (characterset) to another one - Philippe Rocca-Serra - characterset conversion - - - - - - - - - the process of changing the encoding of information from one convention to another one - Philippe Rocca-Serra - encoding conversion - - - - - - - - - the process of changing a numerical representation - Philippe Rocca-Serra - numerical conversion - - - - - - - - - the process of changing a date representation from one convention to another (e.g. from free to ISO8601) - Philippe Rocca-Serra - date conversion - - - - - - - - - the process of changing a numerical representation from one set of units to another one (e.g. from imperial to metric) - Philippe Rocca-Serra - unit conversion - - - - - - - - - the process of dividing the information contained in one element into at least 2 more components - Philippe Rocca-Serra - rule - field splitting - - - - - - - - - the process of bringing information from at least 2 components into one single element (e.g concatenation operation) - Philippe Rocca-Serra - rule - field merging - - - - - - - - - online analytical processing is the process which concerns itself with analyzing multidimensional data interactively from multiple perspectives. OLAP consists of three basic analytical operations: consolidation (roll-up), drill-down, and slicing and dicing - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Online_analytical_processing - olap operation - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube pivoting - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube slicing - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube dicing - - - - - - - - - Data integrity is the maintenance of, and the assurance of the accuracy and consistency of, data over its entire life-cycle,[1] and is a critical aspect to the design, implementation and usage of any system which stores, processes, or retrieves data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_integrity - data integrity checking - - - - - - - - - the process of computing a checksum of a digital document for the purpose of allowing data integrity checking during exchange and transmission - Philippe Rocca-Serra - file checksumming - - - - - - - - - the process of encoding digitical information to make it impossible to decipher without a key, known as the encryption key - Philippe Rocca-Serra - encryption - - - - - - - - - Data anonymization is a type of information sanitization whose intent is privacy protection. It is the process of either encrypting or removing personally identifiable information from data sets, so that the people whom the data describe remain anonymous. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_anonymization - anonymization - - - - - - - - - Pseudonymization is a data management and de-identification procedure by which personally identifiable information fields within a data record are replaced by one or more artificial identifiers, or pseudonyms. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Pseudonymization - pseudoanymization - - - - - - - - - Philippe Rocca-Serra - normalization - - - - - - - - - data mapping is the process of creating data element mappings between two distinct data models. Data mapping is used as a first step for a wide variety of data integration tasks, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_mapping - mapping - - - - - - - - - the process of using software agent to perform a mapping task between data models - Philippe Rocca-Serra - automatic schema mapping - - - - - - - - - the process of using human expert to perform a mapping task between data models - Philippe Rocca-Serra - manual schema mapping - - - - - - - - - the process of using software agent to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - automatic ontology mapping - - - - - - - - - the process of using human expert to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - manual ology mapping - - - - - - - - - serialization (or serialisation) is the process of translating data structures or object state into a format that can be stored (for example, in a file or memory buffer) or transmitted (for example, across a network connection link) and reconstructed later (possibly in a different computer environment) - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Serialization - serialization - - - - - - - - - format conversion is a process on changing the representation model used during serialization - Philippe Rocca-Serra - format conversion - - - - - - - - - the process of checking and evaluating - Philippe Rocca-Serra - assessment - - - - - - - - - the process of checking against a set of rules and ensuring those are met - Philippe Rocca-Serra - validation - - - - - - - - - the process of checking against a set of rules which only concerns themselves with the grammar (syntax) but not the context. A syntactically valid document may contain incoherent content (semantic) - Philippe Rocca-Serra - syntactic validation - - - - - - - - - the process of checking against a set of semantic rules to ascertain information content validity (rather than its format) - Philippe Rocca-Serra - semantic validation - - - - - - - - - the process of checking against a set of constraints - Philippe Rocca-Serra - constraint validation - - - - - - - - - an assessment process which ascertain conformance to a set of specifications - Philippe Rocca-Serra - compliance assessment - - - - - - - - - the process of storing and serving data - Philippe Rocca-Serra - data hosting - - - - - - - - - the process of storing and serving files - Philippe Rocca-Serra - file hosting - - - - - - - - - the process of storing and serving semantic artefacts - Philippe Rocca-Serra - ontology hosting - - - - - - - - - the process of handling (minting, serving, deprecating, obsoleting) data item used to denotes and uniquely mark entities: - Philippe Rocca-Serra - identifier management - - - - - - - - - the process of creating an identifier (e.g. DOI) - Philippe Rocca-Serra - identifier minting - - - - - - - - - the process of handling a request formed from an identifier and direct the requesting agent to the relevant content - Philippe Rocca-Serra - identifier resolution - - - - - - - - - the process of provinding a correspondance between identifiers from 2 distinct resources for the equivalent entities - Philippe Rocca-Serra - identifier mapping - - - - - - - - - the process of leaving a marker in a location where a digital record has been withdrawn, in order to signify that the record had previously existed. - Philippe Rocca-Serra - identifier tombstoning - - - - - - - - - the process of preserving data and information in digital form - Philippe Rocca-Serra - data storage - - - - - - - - - a data storage process which uses a relational database management system - Philippe Rocca-Serra - rdbms data storage - - - - - - - - - a data storage process which uses a storage system indexing document directly - Philippe Rocca-Serra - document oriented data storage - - - - - - - - - a data storage process which stored data as a graph based representation (in contrast to table based representation as in RDBMS) - Philippe Rocca-Serra - graph data storage - - - - - - - - - the process of making a data object available to a public - Philippe Rocca-Serra - publication - - - - - - - - - the process of handling managing the evolution and changes to a data object - Philippe Rocca-Serra - versioning - - - - - - - - - an assessment process which focuses solely on data - Philippe Rocca-Serra - data assessment - - - - - - - - - an assessment process which relies on statistical methods and exploration to carry out an evaluation against a set of metrics - Philippe Rocca-Serra - statistical assessment - - - - - - - - - an assessment process carried by a human agent whose domain knowledge is recognized - Philippe Rocca-Serra - domain expert assessment - - - - - - - - - an assessment process carried by a group of human agent whose domain knowledge is recognized - Philippe Rocca-Serra - collegial/community assessment - - - - - - - - - a process which aims to evaluate the quality of an entity - Philippe Rocca-Serra - quality assessment - - - - - - - - - a process in which the delivery of a service or the quality of a product is assessed, and compared with that required. - Philippe Rocca-Serra - quality assurance - - - - - - - - - logical axiom is a rule defined in semantic model to allow for classification by automatic reasoners - Philippe Rocca-Serra - logical axiom - - - - - - - - - a rule which details the specific action which should be performed when a number of conditions are met - Philippe Rocca-Serra - functional rule - - - - - - - - - a rule which explains how to perform a specific curation action (for instance, a numeric conversion or a string replacement) - Philippe Rocca-Serra - curation rule - - - - - - - - - A regular expression, regex or regexp (sometimes called a rational expression) is a sequence of characters that define a search pattern. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Regular_expression - regular expression - - - - - - - - - a rule which explain how to relate one entity from a domain knowledge to another entity in another domain knowledge - Philippe Rocca-Serra - mapping rule - - - - - - - - - Philippe Rocca-Serra - metric - - - - - - - - - Philippe Rocca-Serra - quality metric - - - - - - - - - a textual entity associated with a semantic annotation in the form of an identifier corresponding to a term in an ontology - Philippe Rocca-Serra - ontology tagged entity - - - - - - - - - a textual entity which has been regularized through a curation process involving data transformation such as markup or substitution - Philippe Rocca-Serra - normalized textual entity - - - - - - - - - Philippe Rocca-Serra - file format - - - - - - - - - a file format specification whose rights are only available to the owner and creator of the said specifications - Philippe Rocca-Serra - propriatory file format - - - - - - - - - a file format whose specifications are available freely, with no restriction, allow full appraisal and review - Philippe Rocca-Serra - open file format - - - - - - - - - a file format which complies with a specification - Philippe Rocca-Serra - standard compliant file format - - - - - - - - - a data standard is a information content entity which prescribe syntax or semantic or both for a given domain knowledge - Philippe Rocca-Serra - Philippe Rocca-Serra - data standard - - - - - - - - - a standardized non-executable file type used by computer software as a pre-formatted example on which to base other files, especially documents - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Template_(file_format) - template - - - - - - - - - a template devised as a blueprint for operation such as extract transform load or similar data transformations - Philippe Rocca-Serra - Philippe Rocca-Serra - transformation template - - - - - - - - - a template devised for a regularized collection of annotation. - Philippe Rocca-Serra - Philippe Rocca-Serra - metadata acquisition template - - - - - - - - - a template devised for a regularized collection of annotated datasets - Philippe Rocca-Serra - data acquisition template - - - - - - - - - is a purpose-built database for the storage and retrieval of triples[1] through semantic queries. A triple is a data entity composed of subject-predicate-object, like "Bob is 35" or "Bob knows Fred". - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Triplestore - RDF triple store - - - - - - - - - knowledge model is an information content entity which corresponds to a representation of domain of human - Philippe Rocca-Serra - knowledge model - - - - - - - - - An entity‚Äìrelationship model (or ER model) describes interrelated things of interest in a specific domain of knowledge. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Conceptual_model#Data_models - object model - - - - - - - - - an object model following unified modeling language formalization - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Entity%E2%80%93relationship_model - uml model - - - - - - - - - Semantic data model is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Semantic_data_model - semantic data model - - - - - - - - - A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of sample data (and similar data from a larger population). A statistical model represents, often in considerably idealized form, the data-generating process. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Statistical_model - statistical model - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - talend - - - - - - - - - a software service for performing curation services powered by machine learning techniques. - Philippe Rocca-Serra - tamr - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - trifacta - - - - - - - - - a software service for data curation and data cleanup provided by Google software company - Philippe Rocca-Serra - google refine - - - - - - - - - a software service for data storage and data mining provided by Google software company - Philippe Rocca-Serra - google bigtable - - - - - - - - - a software service for data curation and data cleaning provided by Amazon software company - Philippe Rocca-Serra - amazon comprehend - - - - - - - - - a software service for data storage and data mining provided by Amazon software company - Philippe Rocca-Serra - amazon redshift - - - - - - - - - a software service for data storage and data mining provided by Microsoft software company and the Azure cloud solution - Philippe Rocca-Serra - microsoft azure - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - tableau - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - penthaho kettle - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - sisense - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - elsevier - - - - - - - - - a software service which offers support for semantic and knowledge management - Philippe Rocca-Serra - poolparty - - - - - - - - - a software service provided by SciBite company to manage controlled terminologies and curation function, combining functions equivalent to OLS,zooma and oxo - Philippe Rocca-Serra - centinel - - - - - - - - - a software service provided by EMBL-EBI SOFT group, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ontology lookup service - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which assist curation based on prior of existing curated and annotated dataset from ArrayExpress database - Philippe Rocca-Serra - zooma - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which serves mapping between ontologies - Philippe Rocca-Serra - oxo - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ncbo bioportal - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies which, given a body of text and a set of ontologies will return annotation hits. - Philippe Rocca-Serra - ncbo annotator - - - - - - - - - a process of choosing or granting a license to an entity (software, hardware,data) - licensing - - - - - - - - - a process which aim to ensure continuation, persistance of a service or structure at minima to maintain its existence and availability. - Philippe Rocca-Serra - maintenance - - - - - - - - - a process which defines how means are assigned to people or organization to execute a task - Philippe Rocca-Serra - resource allocation - - - - - - - - - Philippe Rocca-Serra - team organization - - - - - - - - - a process which consists in estimating the performance of a process based on value addition generated by said process - Philippe Rocca-Serra - value based assessment - - - - - - - - - a rule deterrmine who, when, what and how entities may be made available. - Philippe Rocca-Serra - access condition - - - - - - - - - an access protocol is a software specification defining the implementation for obtaining data under a number of access conditions - Philippe Rocca-Serra - access protocol - - - - - - - - - file transfer protocol is a standard network protocol used for the transfer of computer files between a client and server on a computer network. FTP specifications evolved from the initial RFC114 from 1971 to the latest specification RFC2428 adding support for IPv6 in 1998. - Wikipedia - ftp - - - - - - - - - The Hypertext Transfer Protocol (HTTP) is an application protocol for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web. It is an international standard specified by RFC 2068 in 1997 (HTTP1.1), obsoleted by RFC 2616 in 1999, which was likewise replaced by the RFC 7230 family of RFCs in 2014. - Wikipedia - http - - - - - - - - - secure file transfer protocol is a secured version of the FTP procotol, which relies on SSH authentication - Wikipedia - sftp - - - - - - - - - An application programming interface (API) is a computing interface which defines interactions between multiple software intermediaries - Wikipedia - application programming interface - - - - - - - - - Representational state transfer (REST) is a software architectural style that defines a set of constraints to be used for creating Web services, introduced and defined in 2000 by Roy Fielding in his doctoral dissertation. HTTP-based RESTful APIs are defined with the following aspects: - --a base URI, such as http://api.example.com/collection/; --standard HTTP methods (e.g., GET, POST, PUT, PATCH and DELETE); --a media type that defines state transition data elements - Philippe Rocca-Serra - rest api - - - - - - - - - SOAP (abbreviation for Simple Object Access Protocol) is a messaging protocol specification for exchanging structured information in the implementation of web services in computer networks. Its purpose is to provide extensibility, neutrality, verbosity and independence.[vague] It uses XML Information Set for its message format, and relies on application layer protocols, most often Hypertext Transfer Protocol (HTTP), although some legacy systems communicate over Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission - Wikipedia - soap api - - - - - - - - - The OpenAPI Specification, originally known as the Swagger Specification, is a specification for machine-readable interface files for describing, producing, consuming, and visualizing RESTful web services. - Wikipedia - open/smart api - - - - - - - - - an API which is built using the GraphQL is a query language, a specification, and a set of tools that operates over a single endpoint using HTTP. It is meant to address the issue of "over and under fetching" during querying REST endpoints. GraphQL language was developed by Facebook. (https://www.howtographql.com/basics/1-graphql-is-the-better-rest/) - Philippe Rocca-Serra - graphql api - - - - - - - - - a quality to indicate the stage at which an entity is in its life cycle - Philippe Rocca-Serra - maturity level - - - - - - - - - a maturity level with indicates an early phase, for feasability study capability - Philippe Rocca-Serra - exploratory - - - - - - - - - a maturity level with indicates an early phase, for evaluation and testing assessment capability - Philippe Rocca-Serra - prototypic - - - - - - - - - a maturity level which indicates developing capability which has not reached full potential - Philippe Rocca-Serra - immature - - - - - - - - - a maturity level which indicates a stable, fully fledged capability - Philippe Rocca-Serra - mature - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment capability - Philippe Rocca-Serra - production grade - - - - - - - - - a maturity level which indicates a reference status for a capability in its domain. - Philippe Rocca-Serra - state of the art - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment - Philippe Rocca-Serra - deployed - - - - - - - - - a maturity level which indicates declining capability - Philippe Rocca-Serra - obsolescent - - - - - - - - - a maturity level which indicates a capability has reached the end of its life. - Philippe Rocca-Serra - obsolete - - - - - - - - - a maturity level which indicates a capability has been removed from frontline production. - Philippe Rocca-Serra - retired - - - - - - - - - Data is managed as a requirement to support the analytical workflows of the project, focused on delivering its own results' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_1 - - - - - - - - - Data is managed as a critical research data asset. Achieve a level of management that enables project to efficiently use and manipulate its data assets' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_2 - - - - - - - - - Data is managed according to community standards with re-usability beyond the project scope in mind' - https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_3 - - - - - - - - - Usability and Applicability of Data for use and re-use is measured against metrics to evaluate the implemented processes of the data management environment' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_4 - - - - - - - - - The Environment processes are considered community best practices for FAIR data management' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_5 - - - - - - - - - a quality to indicate the size of the grain in the physical world. by abstraction, a quality to indicate how atomic an entity is. - granularity level - - - - - - - - - a quality to indicate a small size of the entities making up an assembly. - fine - - - - - - - - - a quality to indicate a lack of refinement of the entities making up an assembly. - coarse - - - - - - - - - a quality to indicate the medium size of the entities making up an assembly. - intermediate - - - - - - - - - a quality to indicate how easy or hard it is to locate/find an entity - findability - - - - - - - - - a quality to indicate that an information entity is indexed by global search engines such as Bing,Google,Yandex,DuckDuckGo..) - search engine referenced - - - - - - - - - a quality to indicate that an information entity is markup with schema.org ontology terms - schema.org annotated - - - - - - - - - a quality to indicate that an information entity is available from a data archive - deposited in public archive - - - - - - - - - a quality to indicate that an information entity is available from a data archive and has been assigned a persistent url - assigned with a persistent http resolveable identifier - - - - - - - - - a quality to indicate that an information entity metadata is conformant to datacite metadata schema and has been assigned a Digital Object Identifier (DOI) - doi-ed - - - - - - - - - a quality to indicate how easy or hard it is to understand how an entity may be access and then access it - accessibility - - - - - - - - - a quality to indicate that no access to the entity is possible other than physical site visit - enclaved - - - - - - - - - a quality to indicate that the entity can only be accessed provided the necessary amount of credentials and authorization - access-controlled - - - - - - - - - a quality to indicate how systems are capable of interacting and working together automatically - interoperability - - - - - - - - - a quality which indicates the entity is conformant to an information specification - standard compliant - - - - - - - - - a quality which indicates the entity is conformant to an information specification as assessed by a certification body - standard certified - - - - - - - - - a quality to indicate how easy or hard it is to mobilize and reuse an information entity , for instance in the context of meta-analysis and data integration. - reusability - - - - - - - - - a role to manage company/organization data to ensure security of electronic information related to the organisation and implement systems to offer efficient analysis, storage and documentation of company records. Reduce costs by identifying bad data practices and replacing them with improved practices. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957283 - data manager - - - - - - - - - a data steward is a role within an organization responsible for utilizing an organization's data governance processes to ensure fitness of data elements - both the content and metadata. - https://en.wikipedia.org/wiki/Data_steward - data steward - - - - - - - - - the role of a personel in charge of performing computational or statistical analysis over company/organisation digital assets and datasets - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957285 - data analyst - - - - - - - - - A data custodian ensures that 1) Access to the data is authorized and controlled. 2)Data stewards are identified for each data set. 3)Technical processes sustain data integrity. 4)Processes exist for data quality issue resolution in partnership with Data Stewards. 5)Technical controls safeguard data. 6)Data added to data sets are consistent with the common data model. 7)Versions of Master Data are maintained along with the history of changes. 8)Change management practices are applied in maintenance of the database. 9)Data content and changes can be audited - https://en.wikipedia.org/wiki/Data_custodian - data custodian - - - - - - - - - the role of a personal to bring expertice and knowledge in a specific domain - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957287 - subject matter export - - - - - - - - - the role of a personel in an organization/company to organization, oversee and decide on all tasks related to data and information management in said organization. The role involves taking executive decisions. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957288 - chief information officer - - - - - - - - - the role of a personel in an organization/company to perform and carry out scientific research - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957289 - scientist/researcher - - - - - - - - - the role of a personel in an organization/company in charge of performing data analysis and research with data, around data and about data to deliver scientific insight to the decision makers. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957290 - data scientist - - - - - - - - - the role of a personel in an organization/company with the power of taking executive decisions - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957291 - decision maker - - - - - - - - - the role of an organization to deliver information technology services. - IT provider - - - - - - - - - the role of a personel in an organization to operate on data once clearance has been obtained from a data controller or data custodian - data processor - - - - - - - - - the role of a personel to supervise, organize and manage protection and privacy of data. - https://ec.europa.eu/info/law/law-topic/data-protection/reform/rules-business-and-organisations/obligations/controller-processor/what-data-controller-or-data-processor_en - data controller - - - - - - - - - the role of a personel to conceive information technology solution and computer code in the form of deployable software. - software engineer - - - - - - - - - the role of a personel to preserve, annotate, archive digital assets produced or purchased by an organization. - data curator - - - - - - - - - a plan documenting the resources and practices, such as ontologies, data formats, information standards and backup, protection measures respectively with the objective of ensuring proper data management. - data management plan - - - - - - - - - a document outlining the semantic resources, terminologies, controlled vocabularies and data format against which curation will be applied. Such document. also specifies the steps requires to version datasets following curation action. - curation policy - - - - - - - - - a data dictionnary is a document listing all the variables and their values sets for categorical variables or numerical ranges of values for continuous values, as well as associated units, formulas for computed derived variables, codes and rules for dealing with missing value. - data dictionary - - - - - - - - - a material transfer agreement (MTA) is a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document. - Wikipedia - material transfer agreement - - - - - - - - - a data access agreement (DAA) is a document to specify the terms under which users are provided access to the specified data, and to obtain explicit acceptance of those terms by a user prior to granting him or her access to the data. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document - data access agreement - - - - - - - diff --git a/build/curatO-merged-with-imports.owl b/build/curatO-merged-with-imports.owl deleted file mode 100644 index e188bc7..0000000 --- a/build/curatO-merged-with-imports.owl +++ /dev/null @@ -1,9634 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - - - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - has measurement unit label - - - - - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. - A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - - denotes - - - - - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point - has coordinate unit label - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - is_specified_input_of - - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - Process - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957282 - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - - - - - - - - - conditional specification - - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 - conditional specification - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI - narrative object - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - - obsolete_artifact - true - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - software - - - - - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - OBI_0000261 - group:OBI - - obsolete2_digital entity - true - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - OBI_0000244 - group:OBI - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - - symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary - symbol - - - - - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - information content entity - - - - - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - Lawrence Hunter - PERSON: Alan Ruttenberg - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - - - - - - - rule - example to be added - - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - Philippe Rocca-Serra - OBI_0500021 - PRS - rule - rule - - - - - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000027 - group:OBI - - obsolete2_report figure - true - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - density plot - Density plot of SSC-H and FSC-H. - - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community - density plot - - - - - - - - - report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - PERSON:Chris Stoeckert - GROUP: OBI - OBI_0000099 - report - - - - - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - OBI_0000222 - group:OBI - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000265 - group:OBI - - obsolete_report table - true - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - - - - - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - OBI_0000195 - group:OBI - - obsolete2_digital document - true - - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - measurement datum - - - - - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - - - - - - conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg - conclusion textual entity - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - Philippe Rocca-Serra - text - textual entity - textual entity - - - - - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - - - - - - table - | T F ---+----- -T | T F -F | F F - - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter - table - - - - - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - publication - A journal article or book - - A document that has been accepted by a publisher - PERSON: Lawrence Hunter - publication - - - - - - - - - - - - - - - publication about an investigation - Most scientific journal articles - - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication - publication about an investigation - - - - - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental procedures - experimental section - methods - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - contributions by the authors - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgements - acknowledgments - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional information - appendix - supplemental information - supplementary material - supporting information - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - - - - - 1 - - - - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. - cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg - one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - mass measurement datum - - - - - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - - - - - - - A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 - postal address - - - - - - - - - email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart - email address - - - - - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - documenting - - - - - - - - - line graph - - A line graph is a type of graph created by connecting a series of data -points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart - line graph - - - - - - - - - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - - A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID - assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - - - - - - A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software application - - - - - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviations - abbreviations list - abbreviations used - list of abbreviations - list of abbreviations used - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - - - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - competing interests - conflict of interest - conflict of interest statement - declaration of competing interests - disclosure of potential conflicts of interest - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - funding - funding information - funding sources - funding statement - funding/support - source of funding - sources of funding - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - footnotes - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - - - identifier - An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - - identifier - - - - - - - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - - - - - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - - - - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - - - - - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - - - - - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - - - - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - - - - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - - - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - - - - - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - - - - - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - - - - - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - - - - - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - - - - - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - - - - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - - - - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - - - - - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - - - - - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - - - - - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - - - - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - - - - - - - EL++ ontology module - EL++ ontology module - - - - - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - - - - - investigation - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - - investigation - - - - - - - - - Philippe Rocca-Serra - organization - - - - - - - - - study design execution - a planned process that carries out a study design - - study design execution - - - - - - - - - data transformation - A planned process that produces output data from input data. - - data transformation - data transformation - - - - - - - - - study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - - study design - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - - mass - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - Philippe Rocca-Serra - recall - - - - - - - - - Philippe Rocca-Serra - F-measure - - - - - - - - - Philippe Rocca-Serra - precision - - - - - - - - - length unit - A unit which is a standard measure of the distance between two points. - - length unit - - - - - - - - - mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. - - mass unit - - - - - - - - - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. - - time unit - - - - - - - - Obsolete Class - - - - - - - - - Natural language processing (NLP) is a process concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Natural_language_processing - natural language processing - - - - - - - - - text mining is the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Text_mining - text mining - novartis:text processing - - - - - - - - - sentence extraction is a technique used for automatic summarization of a text. In this shallow approach, statistical heuristics are used to identify the most salient sentences of a text. Sentence extraction is a low-cost approach compared to more knowledge-intensive deeper approaches which require additional knowledge bases such as ontologies or linguistic knowledge. In short "sentence extraction" works as a filter which allows only important sentences to pass. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Sentence_extraction - sentence extraction - - - - - - - - - string tokenization is the process of demarcating and possibly classifying sections of a string of input characters. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Lexical_analysis#Tokenization - string tokenization - - - - - - - - - the process of identifying an entity and marking it up from a free text input - Philippe Rocca-Serra - FAIRplus - concept recognition - - - - - - - - - Named-entity recognition (NER) (also known as entity identification, entity chunking and entity extraction) is a subtask of information extraction that seeks to locate and classify named entity mentions in unstructured text into pre-defined categories such as the person names, organizations, locations, medical codes, time expressions, quantities, monetary values, percentages, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Named-entity_recognition - entity name recognition - - - - - - - - - part-of-speech tagging (POS tagging or PoS tagging or POST), also called grammatical tagging or word-category disambiguation, is the process of marking up a word in a text (corpus) as corresponding to a particular part of speech,[1] based on both its definition and its context‚Äîi.e., its relationship with adjacent and related words in a phrase, sentence, or paragraph. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Part-of-speech_tagging - part of speech tagging - - - - - - - - - Philippe Rocca-Serra - string matching - - - - - - - - - Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_extraction - information extraction - - - - - - - - - Information management (IM) concerns a cycle of organizational activity: the acquisition of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposition through archiving or deletion. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_management - information management - - - - - - - - - the process of handling (from developing to maintaining and serving) controled vocabularies - Philippe Rocca-Serra - terminology management - - - - - - - - - the process of loading, serving controlled vocabularies and terminologies for access, browsing and selection - Philippe Rocca-Serra - terminology hosting - - - - - - - - - the process of searching a terminology with an input string for matching concepts - Philippe Rocca-Serra - terminology lookup - - - - - - - - - the process of handling (from developing to maintaining and serving) a formal knowledge representation, semantic artefact - Philippe Rocca-Serra - ontology management - - - - - - - - - the process of searching an ontology with an input string for matching concepts - Philippe Rocca-Serra - ontology lookup - - - - - - - - - the process of marking up free text element (tokens, possibly resulting from tokenization) with a controlled term from a semantic artefact - Philippe Rocca-Serra - semantic tagging - semantic markup - - - - - - - - - a search process which relies on ontology to improve retrieval (e.g. query expansion) - Philippe Rocca-Serra - semantic search - - - - - - - - - the process of creating, assembling a formal semantic representation - Philippe Rocca-Serra - ontology development - - - - - - - - - the process of keeping a semantic representation up to date and in keeping with advances in the domain. This covers dealing with term submission, term obsoletion, release and evolution - Philippe Rocca-Serra - ontology maintenance - - - - - - - - - the process of re-arranging, re-engineering a formal semantic representation for optimization purpose, such as promotion of module reuse. - Philippe Rocca-Serra - ontology refactoring - - - - - - - - - the process of creating a formal semantic model from sets of existing modules extracted from other compatible semantic frameworks - Philippe Rocca-Serra - ontology composition - - - - - - - - - the process of augmenting a formal semantic model following batch submission of terms from a domain or modeling of a new domain of knowledge connex to the main them of the ontology - Philippe Rocca-Serra - ontology extension - - - - - - - - - an ontology extension process which happens on the fly, as users come up with the need. This is hard to accomplish as allowing user defined terms at will may lead to inconsistency and breakage. - Philippe Rocca-Serra - ontology dynamic extension - - - - - - - - - the process of formally describing a domain of knowledge - Philippe Rocca-Serra - knowledge representation - - - - - - - - - the process of breaking down a domain of knowledge according to rules - Philippe Rocca-Serra - knowledge formalization - - - - - - - - - the process of representing knowledge using formal rules, known as axiomsm, which allow automatic reasoning and solving - Philippe Rocca-Serra - axiomatic representation - - - - - - - - - the process of developing a domain representation by analysing data. - Philippe Rocca-Serra - data modeling - - - - - - - - - a data model is an information content entity which denotes and describes a domain of knowledge - Philippe Rocca-Serra - data model - - - - - - - - - the process of involving statistical methods, machine learning procedure to build a model which can be used to analysis new datasets and draw conclusions from never seen before data. - Philippe Rocca-Serra - model training - - - - - - - - - the process of classification is the process of identifying to which of a set of categories (sub-populations) a new observation belongs, on the basis of a training set of data containing observations (or instances) whose category membership is known - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/String-searching_algorithm - classification - - - - - - - - - data imputation is the process of replacing missing data with substituted values. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Imputation_(statistics) - data imputation - - - - - - - - - dealing with missing value is a process which aims to address the problems that occur when no data value is stored for the variable in an observation. Missing data are a common occurrence and can have a significant effect on the conclusions that can be drawn from the data. - Philippe Rocca-Serra - dealing with missing value - - - - - - - - - extract, transform, load (ETL) is the general procedure of copying data from one or more sources into a destination system which represents the data differently from the source(s) or in a different context than the source(s). - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Extract,_transform,_load - extract transform load process - - - - - - - - - the process of verifying that a data item supplied matches the specifications it is meant to comply with (e.g. an integer, a string,....) - Philippe Rocca-Serra - data type checking - - - - - - - - - the process of removing redundant entries which add volume without adding value - Philippe Rocca-Serra - duplicate removal - - - - - - - - - Philippe Rocca-Serra - pass through loading - - - - - - - - - the process of assessing the presence of a data item in a existing data strucuture or data storage system - Philippe Rocca-Serra - data lookup - - - - - - - - - the process of changing the encoding of information from one repertoir of characters convention (characterset) to another one - Philippe Rocca-Serra - characterset conversion - - - - - - - - - the process of changing the encoding of information from one convention to another one - Philippe Rocca-Serra - encoding conversion - - - - - - - - - the process of changing a numerical representation - Philippe Rocca-Serra - numerical conversion - - - - - - - - - the process of changing a date representation from one convention to another (e.g. from free to ISO8601) - Philippe Rocca-Serra - date conversion - - - - - - - - - the process of changing a numerical representation from one set of units to another one (e.g. from imperial to metric) - Philippe Rocca-Serra - unit conversion - - - - - - - - - the process of dividing the information contained in one element into at least 2 more components - Philippe Rocca-Serra - rule - field splitting - - - - - - - - - the process of bringing information from at least 2 components into one single element (e.g concatenation operation) - Philippe Rocca-Serra - rule - field merging - - - - - - - - - online analytical processing is the process which concerns itself with analyzing multidimensional data interactively from multiple perspectives. OLAP consists of three basic analytical operations: consolidation (roll-up), drill-down, and slicing and dicing - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Online_analytical_processing - olap operation - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube pivoting - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube slicing - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube dicing - - - - - - - - - Data integrity is the maintenance of, and the assurance of the accuracy and consistency of, data over its entire life-cycle,[1] and is a critical aspect to the design, implementation and usage of any system which stores, processes, or retrieves data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_integrity - data integrity checking - - - - - - - - - the process of computing a checksum of a digital document for the purpose of allowing data integrity checking during exchange and transmission - Philippe Rocca-Serra - file checksumming - - - - - - - - - the process of encoding digitical information to make it impossible to decipher without a key, known as the encryption key - Philippe Rocca-Serra - encryption - - - - - - - - - Data anonymization is a type of information sanitization whose intent is privacy protection. It is the process of either encrypting or removing personally identifiable information from data sets, so that the people whom the data describe remain anonymous. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_anonymization - anonymization - - - - - - - - - Pseudonymization is a data management and de-identification procedure by which personally identifiable information fields within a data record are replaced by one or more artificial identifiers, or pseudonyms. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Pseudonymization - pseudoanymization - - - - - - - - - Philippe Rocca-Serra - normalization - - - - - - - - - data mapping is the process of creating data element mappings between two distinct data models. Data mapping is used as a first step for a wide variety of data integration tasks, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_mapping - mapping - - - - - - - - - the process of using software agent to perform a mapping task between data models - Philippe Rocca-Serra - automatic schema mapping - - - - - - - - - the process of using human expert to perform a mapping task between data models - Philippe Rocca-Serra - manual schema mapping - - - - - - - - - the process of using software agent to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - automatic ontology mapping - - - - - - - - - the process of using human expert to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - manual ology mapping - - - - - - - - - serialization (or serialisation) is the process of translating data structures or object state into a format that can be stored (for example, in a file or memory buffer) or transmitted (for example, across a network connection link) and reconstructed later (possibly in a different computer environment) - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Serialization - serialization - - - - - - - - - format conversion is a process on changing the representation model used during serialization - Philippe Rocca-Serra - format conversion - - - - - - - - - the process of checking and evaluating - Philippe Rocca-Serra - assessment - - - - - - - - - the process of checking against a set of rules and ensuring those are met - Philippe Rocca-Serra - validation - - - - - - - - - the process of checking against a set of rules which only concerns themselves with the grammar (syntax) but not the context. A syntactically valid document may contain incoherent content (semantic) - Philippe Rocca-Serra - syntactic validation - - - - - - - - - the process of checking against a set of semantic rules to ascertain information content validity (rather than its format) - Philippe Rocca-Serra - semantic validation - - - - - - - - - the process of checking against a set of constraints - Philippe Rocca-Serra - constraint validation - - - - - - - - - an assessment process which ascertain conformance to a set of specifications - Philippe Rocca-Serra - compliance assessment - - - - - - - - - the process of storing and serving data - Philippe Rocca-Serra - data hosting - - - - - - - - - the process of storing and serving files - Philippe Rocca-Serra - file hosting - - - - - - - - - the process of storing and serving semantic artefacts - Philippe Rocca-Serra - ontology hosting - - - - - - - - - the process of handling (minting, serving, deprecating, obsoleting) data item used to denotes and uniquely mark entities: - Philippe Rocca-Serra - identifier management - - - - - - - - - the process of creating an identifier (e.g. DOI) - Philippe Rocca-Serra - identifier minting - - - - - - - - - the process of handling a request formed from an identifier and direct the requesting agent to the relevant content - Philippe Rocca-Serra - identifier resolution - - - - - - - - - the process of provinding a correspondance between identifiers from 2 distinct resources for the equivalent entities - Philippe Rocca-Serra - identifier mapping - - - - - - - - - the process of leaving a marker in a location where a digital record has been withdrawn, in order to signify that the record had previously existed. - Philippe Rocca-Serra - identifier tombstoning - - - - - - - - - the process of preserving data and information in digital form - Philippe Rocca-Serra - data storage - - - - - - - - - a data storage process which uses a relational database management system - Philippe Rocca-Serra - rdbms data storage - - - - - - - - - a data storage process which uses a storage system indexing document directly - Philippe Rocca-Serra - document oriented data storage - - - - - - - - - a data storage process which stored data as a graph based representation (in contrast to table based representation as in RDBMS) - Philippe Rocca-Serra - graph data storage - - - - - - - - - the process of making a data object available to a public - Philippe Rocca-Serra - publication - - - - - - - - - the process of handling managing the evolution and changes to a data object - Philippe Rocca-Serra - versioning - - - - - - - - - an assessment process which focuses solely on data - Philippe Rocca-Serra - data assessment - - - - - - - - - an assessment process which relies on statistical methods and exploration to carry out an evaluation against a set of metrics - Philippe Rocca-Serra - statistical assessment - - - - - - - - - an assessment process carried by a human agent whose domain knowledge is recognized - Philippe Rocca-Serra - domain expert assessment - - - - - - - - - an assessment process carried by a group of human agent whose domain knowledge is recognized - Philippe Rocca-Serra - collegial/community assessment - - - - - - - - - a process which aims to evaluate the quality of an entity - Philippe Rocca-Serra - quality assessment - - - - - - - - - a process in which the delivery of a service or the quality of a product is assessed, and compared with that required. - Philippe Rocca-Serra - quality assurance - - - - - - - - - logical axiom is a rule defined in semantic model to allow for classification by automatic reasoners - Philippe Rocca-Serra - logical axiom - - - - - - - - - a rule which details the specific action which should be performed when a number of conditions are met - Philippe Rocca-Serra - functional rule - - - - - - - - - a rule which explains how to perform a specific curation action (for instance, a numeric conversion or a string replacement) - Philippe Rocca-Serra - curation rule - - - - - - - - - A regular expression, regex or regexp (sometimes called a rational expression) is a sequence of characters that define a search pattern. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Regular_expression - regular expression - - - - - - - - - a rule which explain how to relate one entity from a domain knowledge to another entity in another domain knowledge - Philippe Rocca-Serra - mapping rule - - - - - - - - - Philippe Rocca-Serra - metric - - - - - - - - - Philippe Rocca-Serra - quality metric - - - - - - - - - a textual entity associated with a semantic annotation in the form of an identifier corresponding to a term in an ontology - Philippe Rocca-Serra - ontology tagged entity - - - - - - - - - a textual entity which has been regularized through a curation process involving data transformation such as markup or substitution - Philippe Rocca-Serra - normalized textual entity - - - - - - - - - Philippe Rocca-Serra - file format - - - - - - - - - a file format specification whose rights are only available to the owner and creator of the said specifications - Philippe Rocca-Serra - propriatory file format - - - - - - - - - a file format whose specifications are available freely, with no restriction, allow full appraisal and review - Philippe Rocca-Serra - open file format - - - - - - - - - a file format which complies with a specification - Philippe Rocca-Serra - standard compliant file format - - - - - - - - - a data standard is a information content entity which prescribe syntax or semantic or both for a given domain knowledge - Philippe Rocca-Serra - Philippe Rocca-Serra - data standard - - - - - - - - - a standardized non-executable file type used by computer software as a pre-formatted example on which to base other files, especially documents - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Template_(file_format) - template - - - - - - - - - a template devised as a blueprint for operation such as extract transform load or similar data transformations - Philippe Rocca-Serra - Philippe Rocca-Serra - transformation template - - - - - - - - - a template devised for a regularized collection of annotation. - Philippe Rocca-Serra - Philippe Rocca-Serra - metadata acquisition template - - - - - - - - - a template devised for a regularized collection of annotated datasets - Philippe Rocca-Serra - data acquisition template - - - - - - - - - is a purpose-built database for the storage and retrieval of triples[1] through semantic queries. A triple is a data entity composed of subject-predicate-object, like "Bob is 35" or "Bob knows Fred". - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Triplestore - RDF triple store - - - - - - - - - knowledge model is an information content entity which corresponds to a representation of domain of human - Philippe Rocca-Serra - knowledge model - - - - - - - - - An entity‚Äìrelationship model (or ER model) describes interrelated things of interest in a specific domain of knowledge. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Conceptual_model#Data_models - object model - - - - - - - - - an object model following unified modeling language formalization - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Entity%E2%80%93relationship_model - uml model - - - - - - - - - Semantic data model is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Semantic_data_model - semantic data model - - - - - - - - - A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of sample data (and similar data from a larger population). A statistical model represents, often in considerably idealized form, the data-generating process. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Statistical_model - statistical model - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - talend - - - - - - - - - a software service for performing curation services powered by machine learning techniques. - Philippe Rocca-Serra - tamr - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - trifacta - - - - - - - - - a software service for data curation and data cleanup provided by Google software company - Philippe Rocca-Serra - google refine - - - - - - - - - a software service for data storage and data mining provided by Google software company - Philippe Rocca-Serra - google bigtable - - - - - - - - - a software service for data curation and data cleaning provided by Amazon software company - Philippe Rocca-Serra - amazon comprehend - - - - - - - - - a software service for data storage and data mining provided by Amazon software company - Philippe Rocca-Serra - amazon redshift - - - - - - - - - a software service for data storage and data mining provided by Microsoft software company and the Azure cloud solution - Philippe Rocca-Serra - microsoft azure - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - tableau - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - penthaho kettle - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - sisense - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - elsevier - - - - - - - - - a software service which offers support for semantic and knowledge management - Philippe Rocca-Serra - poolparty - - - - - - - - - a software service provided by SciBite company to manage controlled terminologies and curation function, combining functions equivalent to OLS,zooma and oxo - Philippe Rocca-Serra - centinel - - - - - - - - - a software service provided by EMBL-EBI SOFT group, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ontology lookup service - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which assist curation based on prior of existing curated and annotated dataset from ArrayExpress database - Philippe Rocca-Serra - zooma - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which serves mapping between ontologies - Philippe Rocca-Serra - oxo - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ncbo bioportal - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies which, given a body of text and a set of ontologies will return annotation hits. - Philippe Rocca-Serra - ncbo annotator - - - - - - - - - a process of choosing or granting a license to an entity (software, hardware,data) - licensing - - - - - - - - - a process which aim to ensure continuation, persistance of a service or structure at minima to maintain its existence and availability. - Philippe Rocca-Serra - maintenance - - - - - - - - - a process which defines how means are assigned to people or organization to execute a task - Philippe Rocca-Serra - resource allocation - - - - - - - - - Philippe Rocca-Serra - team organization - - - - - - - - - a process which consists in estimating the performance of a process based on value addition generated by said process - Philippe Rocca-Serra - value based assessment - - - - - - - - - a rule deterrmine who, when, what and how entities may be made available. - Philippe Rocca-Serra - access condition - - - - - - - - - an access protocol is a software specification defining the implementation for obtaining data under a number of access conditions - Philippe Rocca-Serra - access protocol - - - - - - - - - file transfer protocol is a standard network protocol used for the transfer of computer files between a client and server on a computer network. FTP specifications evolved from the initial RFC114 from 1971 to the latest specification RFC2428 adding support for IPv6 in 1998. - Wikipedia - ftp - - - - - - - - - The Hypertext Transfer Protocol (HTTP) is an application protocol for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web. It is an international standard specified by RFC 2068 in 1997 (HTTP1.1), obsoleted by RFC 2616 in 1999, which was likewise replaced by the RFC 7230 family of RFCs in 2014. - Wikipedia - http - - - - - - - - - secure file transfer protocol is a secured version of the FTP procotol, which relies on SSH authentication - Wikipedia - sftp - - - - - - - - - An application programming interface (API) is a computing interface which defines interactions between multiple software intermediaries - Wikipedia - application programming interface - - - - - - - - - Representational state transfer (REST) is a software architectural style that defines a set of constraints to be used for creating Web services, introduced and defined in 2000 by Roy Fielding in his doctoral dissertation. HTTP-based RESTful APIs are defined with the following aspects: - --a base URI, such as http://api.example.com/collection/; --standard HTTP methods (e.g., GET, POST, PUT, PATCH and DELETE); --a media type that defines state transition data elements - Philippe Rocca-Serra - rest api - - - - - - - - - SOAP (abbreviation for Simple Object Access Protocol) is a messaging protocol specification for exchanging structured information in the implementation of web services in computer networks. Its purpose is to provide extensibility, neutrality, verbosity and independence.[vague] It uses XML Information Set for its message format, and relies on application layer protocols, most often Hypertext Transfer Protocol (HTTP), although some legacy systems communicate over Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission - Wikipedia - soap api - - - - - - - - - The OpenAPI Specification, originally known as the Swagger Specification, is a specification for machine-readable interface files for describing, producing, consuming, and visualizing RESTful web services. - Wikipedia - open/smart api - - - - - - - - - an API which is built using the GraphQL is a query language, a specification, and a set of tools that operates over a single endpoint using HTTP. It is meant to address the issue of "over and under fetching" during querying REST endpoints. GraphQL language was developed by Facebook. (https://www.howtographql.com/basics/1-graphql-is-the-better-rest/) - Philippe Rocca-Serra - graphql api - - - - - - - - - a quality to indicate the stage at which an entity is in its life cycle - Philippe Rocca-Serra - maturity level - - - - - - - - - a maturity level with indicates an early phase, for feasability study capability - Philippe Rocca-Serra - exploratory - - - - - - - - - a maturity level with indicates an early phase, for evaluation and testing assessment capability - Philippe Rocca-Serra - prototypic - - - - - - - - - a maturity level which indicates developing capability which has not reached full potential - Philippe Rocca-Serra - immature - - - - - - - - - a maturity level which indicates a stable, fully fledged capability - Philippe Rocca-Serra - mature - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment capability - Philippe Rocca-Serra - production grade - - - - - - - - - a maturity level which indicates a reference status for a capability in its domain. - Philippe Rocca-Serra - state of the art - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment - Philippe Rocca-Serra - deployed - - - - - - - - - a maturity level which indicates declining capability - Philippe Rocca-Serra - obsolescent - - - - - - - - - a maturity level which indicates a capability has reached the end of its life. - Philippe Rocca-Serra - obsolete - - - - - - - - - a maturity level which indicates a capability has been removed from frontline production. - Philippe Rocca-Serra - retired - - - - - - - - - Data is managed as a requirement to support the analytical workflows of the project, focused on delivering its own results' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_1 - - - - - - - - - Data is managed as a critical research data asset. Achieve a level of management that enables project to efficiently use and manipulate its data assets' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_2 - - - - - - - - - Data is managed according to community standards with re-usability beyond the project scope in mind' - https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_3 - - - - - - - - - Usability and Applicability of Data for use and re-use is measured against metrics to evaluate the implemented processes of the data management environment' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_4 - - - - - - - - - The Environment processes are considered community best practices for FAIR data management' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_5 - - - - - - - - - a quality to indicate the size of the grain in the physical world. by abstraction, a quality to indicate how atomic an entity is. - granularity level - - - - - - - - - a quality to indicate a small size of the entities making up an assembly. - fine - - - - - - - - - a quality to indicate a lack of refinement of the entities making up an assembly. - coarse - - - - - - - - - a quality to indicate the medium size of the entities making up an assembly. - intermediate - - - - - - - - - a quality to indicate how easy or hard it is to locate/find an entity - findability - - - - - - - - - a quality to indicate that an information entity is indexed by global search engines such as Bing,Google,Yandex,DuckDuckGo..) - search engine referenced - - - - - - - - - a quality to indicate that an information entity is markup with schema.org ontology terms - schema.org annotated - - - - - - - - - a quality to indicate that an information entity is available from a data archive - deposited in public archive - - - - - - - - - a quality to indicate that an information entity is available from a data archive and has been assigned a persistent url - assigned with a persistent http resolveable identifier - - - - - - - - - a quality to indicate that an information entity metadata is conformant to datacite metadata schema and has been assigned a Digital Object Identifier (DOI) - doi-ed - - - - - - - - - a quality to indicate how easy or hard it is to understand how an entity may be access and then access it - accessibility - - - - - - - - - a quality to indicate that no access to the entity is possible other than physical site visit - enclaved - - - - - - - - - a quality to indicate that the entity can only be accessed provided the necessary amount of credentials and authorization - access-controlled - - - - - - - - - a quality to indicate how systems are capable of interacting and working together automatically - interoperability - - - - - - - - - a quality which indicates the entity is conformant to an information specification - standard compliant - - - - - - - - - a quality which indicates the entity is conformant to an information specification as assessed by a certification body - standard certified - - - - - - - - - a quality to indicate how easy or hard it is to mobilize and reuse an information entity , for instance in the context of meta-analysis and data integration. - reusability - - - - - - - - - a role to manage company/organization data to ensure security of electronic information related to the organisation and implement systems to offer efficient analysis, storage and documentation of company records. Reduce costs by identifying bad data practices and replacing them with improved practices. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957283 - data manager - - - - - - - - - a data steward is a role within an organization responsible for utilizing an organization's data governance processes to ensure fitness of data elements - both the content and metadata. - https://en.wikipedia.org/wiki/Data_steward - data steward - - - - - - - - - the role of a personel in charge of performing computational or statistical analysis over company/organisation digital assets and datasets - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957285 - data analyst - - - - - - - - - A data custodian ensures that 1) Access to the data is authorized and controlled. 2)Data stewards are identified for each data set. 3)Technical processes sustain data integrity. 4)Processes exist for data quality issue resolution in partnership with Data Stewards. 5)Technical controls safeguard data. 6)Data added to data sets are consistent with the common data model. 7)Versions of Master Data are maintained along with the history of changes. 8)Change management practices are applied in maintenance of the database. 9)Data content and changes can be audited - https://en.wikipedia.org/wiki/Data_custodian - data custodian - - - - - - - - - the role of a personal to bring expertice and knowledge in a specific domain - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957287 - subject matter export - - - - - - - - - the role of a personel in an organization/company to organization, oversee and decide on all tasks related to data and information management in said organization. The role involves taking executive decisions. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957288 - chief information officer - - - - - - - - - the role of a personel in an organization/company to perform and carry out scientific research - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957289 - scientist/researcher - - - - - - - - - the role of a personel in an organization/company in charge of performing data analysis and research with data, around data and about data to deliver scientific insight to the decision makers. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957290 - data scientist - - - - - - - - - the role of a personel in an organization/company with the power of taking executive decisions - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957291 - decision maker - - - - - - - - - the role of an organization to deliver information technology services. - IT provider - - - - - - - - - the role of a personel in an organization to operate on data once clearance has been obtained from a data controller or data custodian - data processor - - - - - - - - - the role of a personel to supervise, organize and manage protection and privacy of data. - https://ec.europa.eu/info/law/law-topic/data-protection/reform/rules-business-and-organisations/obligations/controller-processor/what-data-controller-or-data-processor_en - data controller - - - - - - - - - the role of a personel to conceive information technology solution and computer code in the form of deployable software. - software engineer - - - - - - - - - the role of a personel to preserve, annotate, archive digital assets produced or purchased by an organization. - data curator - - - - - - - - - a plan documenting the resources and practices, such as ontologies, data formats, information standards and backup, protection measures respectively with the objective of ensuring proper data management. - data management plan - - - - - - - - - a document outlining the semantic resources, terminologies, controlled vocabularies and data format against which curation will be applied. Such document. also specifies the steps requires to version datasets following curation action. - curation policy - - - - - - - - - a data dictionnary is a document listing all the variables and their values sets for categorical variables or numerical ranges of values for continuous values, as well as associated units, formulas for computed derived variables, codes and rules for dealing with missing value. - data dictionary - - - - - - - - - a material transfer agreement (MTA) is a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document. - Wikipedia - material transfer agreement - - - - - - - - - a data access agreement (DAA) is a document to specify the terms under which users are provided access to the specified data, and to obtain explicit acceptance of those terms by a user prior to granting him or her access to the data. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document - data access agreement - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - - obsolete_core - true - - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - A reference to a place on the Earth, by its name or by its geographical location. - geographic location - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/build/curatO-reasoned.owl b/build/curatO-reasoned.owl deleted file mode 100644 index 7650ee4..0000000 --- a/build/curatO-reasoned.owl +++ /dev/null @@ -1,9632 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - - - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - has measurement unit label - - - - - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. - A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - - denotes - - - - - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point - has coordinate unit label - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - is_specified_input_of - - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - Process - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957282 - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - - - - - - - - - conditional specification - - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 - conditional specification - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI - narrative object - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - - obsolete_artifact - true - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - software - - - - - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - OBI_0000261 - group:OBI - - obsolete2_digital entity - true - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - OBI_0000244 - group:OBI - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - - symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary - symbol - - - - - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - information content entity - - - - - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - Lawrence Hunter - PERSON: Alan Ruttenberg - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - - - - - - rule - example to be added - - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - Philippe Rocca-Serra - OBI_0500021 - PRS - rule - rule - - - - - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000027 - group:OBI - - obsolete2_report figure - true - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - density plot - Density plot of SSC-H and FSC-H. - - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community - density plot - - - - - - - - - report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - PERSON:Chris Stoeckert - GROUP: OBI - OBI_0000099 - report - - - - - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - OBI_0000222 - group:OBI - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000265 - group:OBI - - obsolete_report table - true - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - - - - - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - OBI_0000195 - group:OBI - - obsolete2_digital document - true - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - measurement datum - - - - - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - - - - - - conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg - conclusion textual entity - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - Philippe Rocca-Serra - text - textual entity - textual entity - - - - - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - - - - - - table - | T F ---+----- -T | T F -F | F F - - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter - table - - - - - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - publication - A journal article or book - - A document that has been accepted by a publisher - PERSON: Lawrence Hunter - publication - - - - - - - - - - - - - - - publication about an investigation - Most scientific journal articles - - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication - publication about an investigation - - - - - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental procedures - experimental section - methods - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - contributions by the authors - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgements - acknowledgments - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional information - appendix - supplemental information - supplementary material - supporting information - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - - - - - 1 - - - - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. - cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg - one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - mass measurement datum - - - - - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - - - - - - - A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 - postal address - - - - - - - - - email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart - email address - - - - - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - documenting - - - - - - - - - line graph - - A line graph is a type of graph created by connecting a series of data -points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart - line graph - - - - - - - - - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - - A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID - assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - - - - - - A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software application - - - - - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviations - abbreviations list - abbreviations used - list of abbreviations - list of abbreviations used - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - - - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - competing interests - conflict of interest - conflict of interest statement - declaration of competing interests - disclosure of potential conflicts of interest - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - funding - funding information - funding sources - funding statement - funding/support - source of funding - sources of funding - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - footnotes - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - - - identifier - An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - - identifier - - - - - - - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - - - - - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - - - - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - - - - - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - - - - - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - - - - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - - - - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - - - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - - - - - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - - - - - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - - - - - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - - - - - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - - - - - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - - - - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - - - - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - - - - - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - - - - - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - - - - - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - - - - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - - - - - - - EL++ ontology module - EL++ ontology module - - - - - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - - - - - investigation - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - - investigation - - - - - - - - - Philippe Rocca-Serra - organization - - - - - - - - - study design execution - a planned process that carries out a study design - - study design execution - - - - - - - - - data transformation - A planned process that produces output data from input data. - - data transformation - data transformation - - - - - - - - - study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - - study design - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - - mass - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - Philippe Rocca-Serra - recall - - - - - - - - - Philippe Rocca-Serra - F-measure - - - - - - - - - Philippe Rocca-Serra - precision - - - - - - - - - length unit - A unit which is a standard measure of the distance between two points. - - length unit - - - - - - - - - mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. - - mass unit - - - - - - - - - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. - - time unit - - - - - - - - Obsolete Class - - - - - - - - - Natural language processing (NLP) is a process concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Natural_language_processing - natural language processing - - - - - - - - - text mining is the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Text_mining - text mining - novartis:text processing - - - - - - - - - sentence extraction is a technique used for automatic summarization of a text. In this shallow approach, statistical heuristics are used to identify the most salient sentences of a text. Sentence extraction is a low-cost approach compared to more knowledge-intensive deeper approaches which require additional knowledge bases such as ontologies or linguistic knowledge. In short "sentence extraction" works as a filter which allows only important sentences to pass. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Sentence_extraction - sentence extraction - - - - - - - - - string tokenization is the process of demarcating and possibly classifying sections of a string of input characters. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Lexical_analysis#Tokenization - string tokenization - - - - - - - - - the process of identifying an entity and marking it up from a free text input - Philippe Rocca-Serra - FAIRplus - concept recognition - - - - - - - - - Named-entity recognition (NER) (also known as entity identification, entity chunking and entity extraction) is a subtask of information extraction that seeks to locate and classify named entity mentions in unstructured text into pre-defined categories such as the person names, organizations, locations, medical codes, time expressions, quantities, monetary values, percentages, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Named-entity_recognition - entity name recognition - - - - - - - - - part-of-speech tagging (POS tagging or PoS tagging or POST), also called grammatical tagging or word-category disambiguation, is the process of marking up a word in a text (corpus) as corresponding to a particular part of speech,[1] based on both its definition and its context‚Äîi.e., its relationship with adjacent and related words in a phrase, sentence, or paragraph. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Part-of-speech_tagging - part of speech tagging - - - - - - - - - Philippe Rocca-Serra - string matching - - - - - - - - - Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_extraction - information extraction - - - - - - - - - Information management (IM) concerns a cycle of organizational activity: the acquisition of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposition through archiving or deletion. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_management - information management - - - - - - - - - the process of handling (from developing to maintaining and serving) controled vocabularies - Philippe Rocca-Serra - terminology management - - - - - - - - - the process of loading, serving controlled vocabularies and terminologies for access, browsing and selection - Philippe Rocca-Serra - terminology hosting - - - - - - - - - the process of searching a terminology with an input string for matching concepts - Philippe Rocca-Serra - terminology lookup - - - - - - - - - the process of handling (from developing to maintaining and serving) a formal knowledge representation, semantic artefact - Philippe Rocca-Serra - ontology management - - - - - - - - - the process of searching an ontology with an input string for matching concepts - Philippe Rocca-Serra - ontology lookup - - - - - - - - - the process of marking up free text element (tokens, possibly resulting from tokenization) with a controlled term from a semantic artefact - Philippe Rocca-Serra - semantic tagging - semantic markup - - - - - - - - - a search process which relies on ontology to improve retrieval (e.g. query expansion) - Philippe Rocca-Serra - semantic search - - - - - - - - - the process of creating, assembling a formal semantic representation - Philippe Rocca-Serra - ontology development - - - - - - - - - the process of keeping a semantic representation up to date and in keeping with advances in the domain. This covers dealing with term submission, term obsoletion, release and evolution - Philippe Rocca-Serra - ontology maintenance - - - - - - - - - the process of re-arranging, re-engineering a formal semantic representation for optimization purpose, such as promotion of module reuse. - Philippe Rocca-Serra - ontology refactoring - - - - - - - - - the process of creating a formal semantic model from sets of existing modules extracted from other compatible semantic frameworks - Philippe Rocca-Serra - ontology composition - - - - - - - - - the process of augmenting a formal semantic model following batch submission of terms from a domain or modeling of a new domain of knowledge connex to the main them of the ontology - Philippe Rocca-Serra - ontology extension - - - - - - - - - an ontology extension process which happens on the fly, as users come up with the need. This is hard to accomplish as allowing user defined terms at will may lead to inconsistency and breakage. - Philippe Rocca-Serra - ontology dynamic extension - - - - - - - - - the process of formally describing a domain of knowledge - Philippe Rocca-Serra - knowledge representation - - - - - - - - - the process of breaking down a domain of knowledge according to rules - Philippe Rocca-Serra - knowledge formalization - - - - - - - - - the process of representing knowledge using formal rules, known as axiomsm, which allow automatic reasoning and solving - Philippe Rocca-Serra - axiomatic representation - - - - - - - - - the process of developing a domain representation by analysing data. - Philippe Rocca-Serra - data modeling - - - - - - - - - a data model is an information content entity which denotes and describes a domain of knowledge - Philippe Rocca-Serra - data model - - - - - - - - - the process of involving statistical methods, machine learning procedure to build a model which can be used to analysis new datasets and draw conclusions from never seen before data. - Philippe Rocca-Serra - model training - - - - - - - - - the process of classification is the process of identifying to which of a set of categories (sub-populations) a new observation belongs, on the basis of a training set of data containing observations (or instances) whose category membership is known - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/String-searching_algorithm - classification - - - - - - - - - data imputation is the process of replacing missing data with substituted values. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Imputation_(statistics) - data imputation - - - - - - - - - dealing with missing value is a process which aims to address the problems that occur when no data value is stored for the variable in an observation. Missing data are a common occurrence and can have a significant effect on the conclusions that can be drawn from the data. - Philippe Rocca-Serra - dealing with missing value - - - - - - - - - extract, transform, load (ETL) is the general procedure of copying data from one or more sources into a destination system which represents the data differently from the source(s) or in a different context than the source(s). - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Extract,_transform,_load - extract transform load process - - - - - - - - - the process of verifying that a data item supplied matches the specifications it is meant to comply with (e.g. an integer, a string,....) - Philippe Rocca-Serra - data type checking - - - - - - - - - the process of removing redundant entries which add volume without adding value - Philippe Rocca-Serra - duplicate removal - - - - - - - - - Philippe Rocca-Serra - pass through loading - - - - - - - - - the process of assessing the presence of a data item in a existing data strucuture or data storage system - Philippe Rocca-Serra - data lookup - - - - - - - - - the process of changing the encoding of information from one repertoir of characters convention (characterset) to another one - Philippe Rocca-Serra - characterset conversion - - - - - - - - - the process of changing the encoding of information from one convention to another one - Philippe Rocca-Serra - encoding conversion - - - - - - - - - the process of changing a numerical representation - Philippe Rocca-Serra - numerical conversion - - - - - - - - - the process of changing a date representation from one convention to another (e.g. from free to ISO8601) - Philippe Rocca-Serra - date conversion - - - - - - - - - the process of changing a numerical representation from one set of units to another one (e.g. from imperial to metric) - Philippe Rocca-Serra - unit conversion - - - - - - - - - the process of dividing the information contained in one element into at least 2 more components - Philippe Rocca-Serra - rule - field splitting - - - - - - - - - the process of bringing information from at least 2 components into one single element (e.g concatenation operation) - Philippe Rocca-Serra - rule - field merging - - - - - - - - - online analytical processing is the process which concerns itself with analyzing multidimensional data interactively from multiple perspectives. OLAP consists of three basic analytical operations: consolidation (roll-up), drill-down, and slicing and dicing - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Online_analytical_processing - olap operation - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube pivoting - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube slicing - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube dicing - - - - - - - - - Data integrity is the maintenance of, and the assurance of the accuracy and consistency of, data over its entire life-cycle,[1] and is a critical aspect to the design, implementation and usage of any system which stores, processes, or retrieves data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_integrity - data integrity checking - - - - - - - - - the process of computing a checksum of a digital document for the purpose of allowing data integrity checking during exchange and transmission - Philippe Rocca-Serra - file checksumming - - - - - - - - - the process of encoding digitical information to make it impossible to decipher without a key, known as the encryption key - Philippe Rocca-Serra - encryption - - - - - - - - - Data anonymization is a type of information sanitization whose intent is privacy protection. It is the process of either encrypting or removing personally identifiable information from data sets, so that the people whom the data describe remain anonymous. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_anonymization - anonymization - - - - - - - - - Pseudonymization is a data management and de-identification procedure by which personally identifiable information fields within a data record are replaced by one or more artificial identifiers, or pseudonyms. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Pseudonymization - pseudoanymization - - - - - - - - - Philippe Rocca-Serra - normalization - - - - - - - - - data mapping is the process of creating data element mappings between two distinct data models. Data mapping is used as a first step for a wide variety of data integration tasks, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_mapping - mapping - - - - - - - - - the process of using software agent to perform a mapping task between data models - Philippe Rocca-Serra - automatic schema mapping - - - - - - - - - the process of using human expert to perform a mapping task between data models - Philippe Rocca-Serra - manual schema mapping - - - - - - - - - the process of using software agent to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - automatic ontology mapping - - - - - - - - - the process of using human expert to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - manual ology mapping - - - - - - - - - serialization (or serialisation) is the process of translating data structures or object state into a format that can be stored (for example, in a file or memory buffer) or transmitted (for example, across a network connection link) and reconstructed later (possibly in a different computer environment) - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Serialization - serialization - - - - - - - - - format conversion is a process on changing the representation model used during serialization - Philippe Rocca-Serra - format conversion - - - - - - - - - the process of checking and evaluating - Philippe Rocca-Serra - assessment - - - - - - - - - the process of checking against a set of rules and ensuring those are met - Philippe Rocca-Serra - validation - - - - - - - - - the process of checking against a set of rules which only concerns themselves with the grammar (syntax) but not the context. A syntactically valid document may contain incoherent content (semantic) - Philippe Rocca-Serra - syntactic validation - - - - - - - - - the process of checking against a set of semantic rules to ascertain information content validity (rather than its format) - Philippe Rocca-Serra - semantic validation - - - - - - - - - the process of checking against a set of constraints - Philippe Rocca-Serra - constraint validation - - - - - - - - - an assessment process which ascertain conformance to a set of specifications - Philippe Rocca-Serra - compliance assessment - - - - - - - - - the process of storing and serving data - Philippe Rocca-Serra - data hosting - - - - - - - - - the process of storing and serving files - Philippe Rocca-Serra - file hosting - - - - - - - - - the process of storing and serving semantic artefacts - Philippe Rocca-Serra - ontology hosting - - - - - - - - - the process of handling (minting, serving, deprecating, obsoleting) data item used to denotes and uniquely mark entities: - Philippe Rocca-Serra - identifier management - - - - - - - - - the process of creating an identifier (e.g. DOI) - Philippe Rocca-Serra - identifier minting - - - - - - - - - the process of handling a request formed from an identifier and direct the requesting agent to the relevant content - Philippe Rocca-Serra - identifier resolution - - - - - - - - - the process of provinding a correspondance between identifiers from 2 distinct resources for the equivalent entities - Philippe Rocca-Serra - identifier mapping - - - - - - - - - the process of leaving a marker in a location where a digital record has been withdrawn, in order to signify that the record had previously existed. - Philippe Rocca-Serra - identifier tombstoning - - - - - - - - - the process of preserving data and information in digital form - Philippe Rocca-Serra - data storage - - - - - - - - - a data storage process which uses a relational database management system - Philippe Rocca-Serra - rdbms data storage - - - - - - - - - a data storage process which uses a storage system indexing document directly - Philippe Rocca-Serra - document oriented data storage - - - - - - - - - a data storage process which stored data as a graph based representation (in contrast to table based representation as in RDBMS) - Philippe Rocca-Serra - graph data storage - - - - - - - - - the process of making a data object available to a public - Philippe Rocca-Serra - publication - - - - - - - - - the process of handling managing the evolution and changes to a data object - Philippe Rocca-Serra - versioning - - - - - - - - - an assessment process which focuses solely on data - Philippe Rocca-Serra - data assessment - - - - - - - - - an assessment process which relies on statistical methods and exploration to carry out an evaluation against a set of metrics - Philippe Rocca-Serra - statistical assessment - - - - - - - - - an assessment process carried by a human agent whose domain knowledge is recognized - Philippe Rocca-Serra - domain expert assessment - - - - - - - - - an assessment process carried by a group of human agent whose domain knowledge is recognized - Philippe Rocca-Serra - collegial/community assessment - - - - - - - - - a process which aims to evaluate the quality of an entity - Philippe Rocca-Serra - quality assessment - - - - - - - - - a process in which the delivery of a service or the quality of a product is assessed, and compared with that required. - Philippe Rocca-Serra - quality assurance - - - - - - - - - logical axiom is a rule defined in semantic model to allow for classification by automatic reasoners - Philippe Rocca-Serra - logical axiom - - - - - - - - - a rule which details the specific action which should be performed when a number of conditions are met - Philippe Rocca-Serra - functional rule - - - - - - - - - a rule which explains how to perform a specific curation action (for instance, a numeric conversion or a string replacement) - Philippe Rocca-Serra - curation rule - - - - - - - - - A regular expression, regex or regexp (sometimes called a rational expression) is a sequence of characters that define a search pattern. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Regular_expression - regular expression - - - - - - - - - a rule which explain how to relate one entity from a domain knowledge to another entity in another domain knowledge - Philippe Rocca-Serra - mapping rule - - - - - - - - - Philippe Rocca-Serra - metric - - - - - - - - - Philippe Rocca-Serra - quality metric - - - - - - - - - a textual entity associated with a semantic annotation in the form of an identifier corresponding to a term in an ontology - Philippe Rocca-Serra - ontology tagged entity - - - - - - - - - a textual entity which has been regularized through a curation process involving data transformation such as markup or substitution - Philippe Rocca-Serra - normalized textual entity - - - - - - - - - Philippe Rocca-Serra - file format - - - - - - - - - a file format specification whose rights are only available to the owner and creator of the said specifications - Philippe Rocca-Serra - propriatory file format - - - - - - - - - a file format whose specifications are available freely, with no restriction, allow full appraisal and review - Philippe Rocca-Serra - open file format - - - - - - - - - a file format which complies with a specification - Philippe Rocca-Serra - standard compliant file format - - - - - - - - - a data standard is a information content entity which prescribe syntax or semantic or both for a given domain knowledge - Philippe Rocca-Serra - Philippe Rocca-Serra - data standard - - - - - - - - - a standardized non-executable file type used by computer software as a pre-formatted example on which to base other files, especially documents - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Template_(file_format) - template - - - - - - - - - a template devised as a blueprint for operation such as extract transform load or similar data transformations - Philippe Rocca-Serra - Philippe Rocca-Serra - transformation template - - - - - - - - - a template devised for a regularized collection of annotation. - Philippe Rocca-Serra - Philippe Rocca-Serra - metadata acquisition template - - - - - - - - - a template devised for a regularized collection of annotated datasets - Philippe Rocca-Serra - data acquisition template - - - - - - - - - is a purpose-built database for the storage and retrieval of triples[1] through semantic queries. A triple is a data entity composed of subject-predicate-object, like "Bob is 35" or "Bob knows Fred". - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Triplestore - RDF triple store - - - - - - - - - knowledge model is an information content entity which corresponds to a representation of domain of human - Philippe Rocca-Serra - knowledge model - - - - - - - - - An entity‚Äìrelationship model (or ER model) describes interrelated things of interest in a specific domain of knowledge. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Conceptual_model#Data_models - object model - - - - - - - - - an object model following unified modeling language formalization - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Entity%E2%80%93relationship_model - uml model - - - - - - - - - Semantic data model is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Semantic_data_model - semantic data model - - - - - - - - - A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of sample data (and similar data from a larger population). A statistical model represents, often in considerably idealized form, the data-generating process. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Statistical_model - statistical model - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - talend - - - - - - - - - a software service for performing curation services powered by machine learning techniques. - Philippe Rocca-Serra - tamr - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - trifacta - - - - - - - - - a software service for data curation and data cleanup provided by Google software company - Philippe Rocca-Serra - google refine - - - - - - - - - a software service for data storage and data mining provided by Google software company - Philippe Rocca-Serra - google bigtable - - - - - - - - - a software service for data curation and data cleaning provided by Amazon software company - Philippe Rocca-Serra - amazon comprehend - - - - - - - - - a software service for data storage and data mining provided by Amazon software company - Philippe Rocca-Serra - amazon redshift - - - - - - - - - a software service for data storage and data mining provided by Microsoft software company and the Azure cloud solution - Philippe Rocca-Serra - microsoft azure - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - tableau - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - penthaho kettle - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - sisense - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - elsevier - - - - - - - - - a software service which offers support for semantic and knowledge management - Philippe Rocca-Serra - poolparty - - - - - - - - - a software service provided by SciBite company to manage controlled terminologies and curation function, combining functions equivalent to OLS,zooma and oxo - Philippe Rocca-Serra - centinel - - - - - - - - - a software service provided by EMBL-EBI SOFT group, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ontology lookup service - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which assist curation based on prior of existing curated and annotated dataset from ArrayExpress database - Philippe Rocca-Serra - zooma - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which serves mapping between ontologies - Philippe Rocca-Serra - oxo - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ncbo bioportal - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies which, given a body of text and a set of ontologies will return annotation hits. - Philippe Rocca-Serra - ncbo annotator - - - - - - - - - a process of choosing or granting a license to an entity (software, hardware,data) - licensing - - - - - - - - - a process which aim to ensure continuation, persistance of a service or structure at minima to maintain its existence and availability. - Philippe Rocca-Serra - maintenance - - - - - - - - - a process which defines how means are assigned to people or organization to execute a task - Philippe Rocca-Serra - resource allocation - - - - - - - - - Philippe Rocca-Serra - team organization - - - - - - - - - a process which consists in estimating the performance of a process based on value addition generated by said process - Philippe Rocca-Serra - value based assessment - - - - - - - - - a rule deterrmine who, when, what and how entities may be made available. - Philippe Rocca-Serra - access condition - - - - - - - - - an access protocol is a software specification defining the implementation for obtaining data under a number of access conditions - Philippe Rocca-Serra - access protocol - - - - - - - - - file transfer protocol is a standard network protocol used for the transfer of computer files between a client and server on a computer network. FTP specifications evolved from the initial RFC114 from 1971 to the latest specification RFC2428 adding support for IPv6 in 1998. - Wikipedia - ftp - - - - - - - - - The Hypertext Transfer Protocol (HTTP) is an application protocol for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web. It is an international standard specified by RFC 2068 in 1997 (HTTP1.1), obsoleted by RFC 2616 in 1999, which was likewise replaced by the RFC 7230 family of RFCs in 2014. - Wikipedia - http - - - - - - - - - secure file transfer protocol is a secured version of the FTP procotol, which relies on SSH authentication - Wikipedia - sftp - - - - - - - - - An application programming interface (API) is a computing interface which defines interactions between multiple software intermediaries - Wikipedia - application programming interface - - - - - - - - - Representational state transfer (REST) is a software architectural style that defines a set of constraints to be used for creating Web services, introduced and defined in 2000 by Roy Fielding in his doctoral dissertation. HTTP-based RESTful APIs are defined with the following aspects: - --a base URI, such as http://api.example.com/collection/; --standard HTTP methods (e.g., GET, POST, PUT, PATCH and DELETE); --a media type that defines state transition data elements - Philippe Rocca-Serra - rest api - - - - - - - - - SOAP (abbreviation for Simple Object Access Protocol) is a messaging protocol specification for exchanging structured information in the implementation of web services in computer networks. Its purpose is to provide extensibility, neutrality, verbosity and independence.[vague] It uses XML Information Set for its message format, and relies on application layer protocols, most often Hypertext Transfer Protocol (HTTP), although some legacy systems communicate over Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission - Wikipedia - soap api - - - - - - - - - The OpenAPI Specification, originally known as the Swagger Specification, is a specification for machine-readable interface files for describing, producing, consuming, and visualizing RESTful web services. - Wikipedia - open/smart api - - - - - - - - - an API which is built using the GraphQL is a query language, a specification, and a set of tools that operates over a single endpoint using HTTP. It is meant to address the issue of "over and under fetching" during querying REST endpoints. GraphQL language was developed by Facebook. (https://www.howtographql.com/basics/1-graphql-is-the-better-rest/) - Philippe Rocca-Serra - graphql api - - - - - - - - - a quality to indicate the stage at which an entity is in its life cycle - Philippe Rocca-Serra - maturity level - - - - - - - - - a maturity level with indicates an early phase, for feasability study capability - Philippe Rocca-Serra - exploratory - - - - - - - - - a maturity level with indicates an early phase, for evaluation and testing assessment capability - Philippe Rocca-Serra - prototypic - - - - - - - - - a maturity level which indicates developing capability which has not reached full potential - Philippe Rocca-Serra - immature - - - - - - - - - a maturity level which indicates a stable, fully fledged capability - Philippe Rocca-Serra - mature - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment capability - Philippe Rocca-Serra - production grade - - - - - - - - - a maturity level which indicates a reference status for a capability in its domain. - Philippe Rocca-Serra - state of the art - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment - Philippe Rocca-Serra - deployed - - - - - - - - - a maturity level which indicates declining capability - Philippe Rocca-Serra - obsolescent - - - - - - - - - a maturity level which indicates a capability has reached the end of its life. - Philippe Rocca-Serra - obsolete - - - - - - - - - a maturity level which indicates a capability has been removed from frontline production. - Philippe Rocca-Serra - retired - - - - - - - - - Data is managed as a requirement to support the analytical workflows of the project, focused on delivering its own results' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_1 - - - - - - - - - Data is managed as a critical research data asset. Achieve a level of management that enables project to efficiently use and manipulate its data assets' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_2 - - - - - - - - - Data is managed according to community standards with re-usability beyond the project scope in mind' - https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_3 - - - - - - - - - Usability and Applicability of Data for use and re-use is measured against metrics to evaluate the implemented processes of the data management environment' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_4 - - - - - - - - - The Environment processes are considered community best practices for FAIR data management' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_5 - - - - - - - - - a quality to indicate the size of the grain in the physical world. by abstraction, a quality to indicate how atomic an entity is. - granularity level - - - - - - - - - a quality to indicate a small size of the entities making up an assembly. - fine - - - - - - - - - a quality to indicate a lack of refinement of the entities making up an assembly. - coarse - - - - - - - - - a quality to indicate the medium size of the entities making up an assembly. - intermediate - - - - - - - - - a quality to indicate how easy or hard it is to locate/find an entity - findability - - - - - - - - - a quality to indicate that an information entity is indexed by global search engines such as Bing,Google,Yandex,DuckDuckGo..) - search engine referenced - - - - - - - - - a quality to indicate that an information entity is markup with schema.org ontology terms - schema.org annotated - - - - - - - - - a quality to indicate that an information entity is available from a data archive - deposited in public archive - - - - - - - - - a quality to indicate that an information entity is available from a data archive and has been assigned a persistent url - assigned with a persistent http resolveable identifier - - - - - - - - - a quality to indicate that an information entity metadata is conformant to datacite metadata schema and has been assigned a Digital Object Identifier (DOI) - doi-ed - - - - - - - - - a quality to indicate how easy or hard it is to understand how an entity may be access and then access it - accessibility - - - - - - - - - a quality to indicate that no access to the entity is possible other than physical site visit - enclaved - - - - - - - - - a quality to indicate that the entity can only be accessed provided the necessary amount of credentials and authorization - access-controlled - - - - - - - - - a quality to indicate how systems are capable of interacting and working together automatically - interoperability - - - - - - - - - a quality which indicates the entity is conformant to an information specification - standard compliant - - - - - - - - - a quality which indicates the entity is conformant to an information specification as assessed by a certification body - standard certified - - - - - - - - - a quality to indicate how easy or hard it is to mobilize and reuse an information entity , for instance in the context of meta-analysis and data integration. - reusability - - - - - - - - - a role to manage company/organization data to ensure security of electronic information related to the organisation and implement systems to offer efficient analysis, storage and documentation of company records. Reduce costs by identifying bad data practices and replacing them with improved practices. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957283 - data manager - - - - - - - - - a data steward is a role within an organization responsible for utilizing an organization's data governance processes to ensure fitness of data elements - both the content and metadata. - https://en.wikipedia.org/wiki/Data_steward - data steward - - - - - - - - - the role of a personel in charge of performing computational or statistical analysis over company/organisation digital assets and datasets - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957285 - data analyst - - - - - - - - - A data custodian ensures that 1) Access to the data is authorized and controlled. 2)Data stewards are identified for each data set. 3)Technical processes sustain data integrity. 4)Processes exist for data quality issue resolution in partnership with Data Stewards. 5)Technical controls safeguard data. 6)Data added to data sets are consistent with the common data model. 7)Versions of Master Data are maintained along with the history of changes. 8)Change management practices are applied in maintenance of the database. 9)Data content and changes can be audited - https://en.wikipedia.org/wiki/Data_custodian - data custodian - - - - - - - - - the role of a personal to bring expertice and knowledge in a specific domain - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957287 - subject matter export - - - - - - - - - the role of a personel in an organization/company to organization, oversee and decide on all tasks related to data and information management in said organization. The role involves taking executive decisions. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957288 - chief information officer - - - - - - - - - the role of a personel in an organization/company to perform and carry out scientific research - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957289 - scientist/researcher - - - - - - - - - the role of a personel in an organization/company in charge of performing data analysis and research with data, around data and about data to deliver scientific insight to the decision makers. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957290 - data scientist - - - - - - - - - the role of a personel in an organization/company with the power of taking executive decisions - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957291 - decision maker - - - - - - - - - the role of an organization to deliver information technology services. - IT provider - - - - - - - - - the role of a personel in an organization to operate on data once clearance has been obtained from a data controller or data custodian - data processor - - - - - - - - - the role of a personel to supervise, organize and manage protection and privacy of data. - https://ec.europa.eu/info/law/law-topic/data-protection/reform/rules-business-and-organisations/obligations/controller-processor/what-data-controller-or-data-processor_en - data controller - - - - - - - - - the role of a personel to conceive information technology solution and computer code in the form of deployable software. - software engineer - - - - - - - - - the role of a personel to preserve, annotate, archive digital assets produced or purchased by an organization. - data curator - - - - - - - - - a plan documenting the resources and practices, such as ontologies, data formats, information standards and backup, protection measures respectively with the objective of ensuring proper data management. - data management plan - - - - - - - - - a document outlining the semantic resources, terminologies, controlled vocabularies and data format against which curation will be applied. Such document. also specifies the steps requires to version datasets following curation action. - curation policy - - - - - - - - - a data dictionnary is a document listing all the variables and their values sets for categorical variables or numerical ranges of values for continuous values, as well as associated units, formulas for computed derived variables, codes and rules for dealing with missing value. - data dictionary - - - - - - - - - a material transfer agreement (MTA) is a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document. - Wikipedia - material transfer agreement - - - - - - - - - a data access agreement (DAA) is a document to specify the terms under which users are provided access to the specified data, and to obtain explicit acceptance of those terms by a user prior to granting him or her access to the data. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document - data access agreement - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - - obsolete_core - true - - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - A reference to a place on the Earth, by its name or by its geographical location. - geographic location - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/build/curatO.owl b/build/curatO.owl deleted file mode 100644 index cedde11..0000000 --- a/build/curatO.owl +++ /dev/null @@ -1,9647 +0,0 @@ - - - - - Andrea Splendiani - Carole Goble - Danielle Welter - Fuqi Xu - Ibrahim Iemam - Nick Juty - Oya Deniz Beyan - Philippe Rocca-Serra - an ontology to support FAIR Maturity Evaluation. produced by IMI FAIRplus Consortium - http://creativecommons.org/licenses/by/4.0/ - curatO - Comment from annotations.ttl file. - 2020-09-09 - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - - - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - has measurement unit label - - - - - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. - A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - - denotes - - - - - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point - has coordinate unit label - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - is_specified_input_of - - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - Process - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957282 - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - - - - - - - - - conditional specification - - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 - conditional specification - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI - narrative object - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - - obsolete_artifact - true - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - software - - - - - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - OBI_0000261 - group:OBI - - obsolete2_digital entity - true - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - OBI_0000244 - group:OBI - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - - symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary - symbol - - - - - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - information content entity - - - - - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - Lawrence Hunter - PERSON: Alan Ruttenberg - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - - - - - - rule - example to be added - - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - Philippe Rocca-Serra - OBI_0500021 - PRS - rule - rule - - - - - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000027 - group:OBI - - obsolete2_report figure - true - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - density plot - Density plot of SSC-H and FSC-H. - - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community - density plot - - - - - - - - - report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - PERSON:Chris Stoeckert - GROUP: OBI - OBI_0000099 - report - - - - - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - OBI_0000222 - group:OBI - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000265 - group:OBI - - obsolete_report table - true - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - - - - - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - OBI_0000195 - group:OBI - - obsolete2_digital document - true - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - measurement datum - - - - - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - - - - - - conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg - conclusion textual entity - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - Philippe Rocca-Serra - text - textual entity - textual entity - - - - - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - - - - - - table - | T F ---+----- -T | T F -F | F F - - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter - table - - - - - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - publication - A journal article or book - - A document that has been accepted by a publisher - PERSON: Lawrence Hunter - publication - - - - - - - - - - - - - - - publication about an investigation - Most scientific journal articles - - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication - publication about an investigation - - - - - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental procedures - experimental section - methods - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - contributions by the authors - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgements - acknowledgments - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional information - appendix - supplemental information - supplementary material - supporting information - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - - - - - 1 - - - - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. - cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg - one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - mass measurement datum - - - - - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - - - - - - - A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 - postal address - - - - - - - - - email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart - email address - - - - - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - documenting - - - - - - - - - line graph - - A line graph is a type of graph created by connecting a series of data -points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart - line graph - - - - - - - - - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - - A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID - assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - - - - - - A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software application - - - - - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviations - abbreviations list - abbreviations used - list of abbreviations - list of abbreviations used - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - - - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - competing interests - conflict of interest - conflict of interest statement - declaration of competing interests - disclosure of potential conflicts of interest - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - funding - funding information - funding sources - funding statement - funding/support - source of funding - sources of funding - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - footnotes - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - - - identifier - An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - - identifier - - - - - - - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - - - - - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - - - - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - - - - - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - - - - - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - - - - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - - - - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - - - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - - - - - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - - - - - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - - - - - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - - - - - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - - - - - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - - - - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - - - - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - - - - - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - - - - - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - - - - - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - - - - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - - - - - - - EL++ ontology module - EL++ ontology module - - - - - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - - - - - investigation - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - - investigation - - - - - - - - - Philippe Rocca-Serra - organization - - - - - - - - - study design execution - a planned process that carries out a study design - - study design execution - - - - - - - - - data transformation - A planned process that produces output data from input data. - - data transformation - data transformation - - - - - - - - - study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - - study design - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - - mass - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - Philippe Rocca-Serra - recall - - - - - - - - - Philippe Rocca-Serra - F-measure - - - - - - - - - Philippe Rocca-Serra - precision - - - - - - - - - length unit - A unit which is a standard measure of the distance between two points. - - length unit - - - - - - - - - mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. - - mass unit - - - - - - - - - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. - - time unit - - - - - - - - Obsolete Class - - - - - - - - - Natural language processing (NLP) is a process concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Natural_language_processing - natural language processing - - - - - - - - - text mining is the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Text_mining - text mining - novartis:text processing - - - - - - - - - sentence extraction is a technique used for automatic summarization of a text. In this shallow approach, statistical heuristics are used to identify the most salient sentences of a text. Sentence extraction is a low-cost approach compared to more knowledge-intensive deeper approaches which require additional knowledge bases such as ontologies or linguistic knowledge. In short "sentence extraction" works as a filter which allows only important sentences to pass. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Sentence_extraction - sentence extraction - - - - - - - - - string tokenization is the process of demarcating and possibly classifying sections of a string of input characters. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Lexical_analysis#Tokenization - string tokenization - - - - - - - - - the process of identifying an entity and marking it up from a free text input - Philippe Rocca-Serra - FAIRplus - concept recognition - - - - - - - - - Named-entity recognition (NER) (also known as entity identification, entity chunking and entity extraction) is a subtask of information extraction that seeks to locate and classify named entity mentions in unstructured text into pre-defined categories such as the person names, organizations, locations, medical codes, time expressions, quantities, monetary values, percentages, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Named-entity_recognition - entity name recognition - - - - - - - - - part-of-speech tagging (POS tagging or PoS tagging or POST), also called grammatical tagging or word-category disambiguation, is the process of marking up a word in a text (corpus) as corresponding to a particular part of speech,[1] based on both its definition and its context‚Äîi.e., its relationship with adjacent and related words in a phrase, sentence, or paragraph. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Part-of-speech_tagging - part of speech tagging - - - - - - - - - Philippe Rocca-Serra - string matching - - - - - - - - - Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_extraction - information extraction - - - - - - - - - Information management (IM) concerns a cycle of organizational activity: the acquisition of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposition through archiving or deletion. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Information_management - information management - - - - - - - - - the process of handling (from developing to maintaining and serving) controled vocabularies - Philippe Rocca-Serra - terminology management - - - - - - - - - the process of loading, serving controlled vocabularies and terminologies for access, browsing and selection - Philippe Rocca-Serra - terminology hosting - - - - - - - - - the process of searching a terminology with an input string for matching concepts - Philippe Rocca-Serra - terminology lookup - - - - - - - - - the process of handling (from developing to maintaining and serving) a formal knowledge representation, semantic artefact - Philippe Rocca-Serra - ontology management - - - - - - - - - the process of searching an ontology with an input string for matching concepts - Philippe Rocca-Serra - ontology lookup - - - - - - - - - the process of marking up free text element (tokens, possibly resulting from tokenization) with a controlled term from a semantic artefact - Philippe Rocca-Serra - semantic tagging - semantic markup - - - - - - - - - a search process which relies on ontology to improve retrieval (e.g. query expansion) - Philippe Rocca-Serra - semantic search - - - - - - - - - the process of creating, assembling a formal semantic representation - Philippe Rocca-Serra - ontology development - - - - - - - - - the process of keeping a semantic representation up to date and in keeping with advances in the domain. This covers dealing with term submission, term obsoletion, release and evolution - Philippe Rocca-Serra - ontology maintenance - - - - - - - - - the process of re-arranging, re-engineering a formal semantic representation for optimization purpose, such as promotion of module reuse. - Philippe Rocca-Serra - ontology refactoring - - - - - - - - - the process of creating a formal semantic model from sets of existing modules extracted from other compatible semantic frameworks - Philippe Rocca-Serra - ontology composition - - - - - - - - - the process of augmenting a formal semantic model following batch submission of terms from a domain or modeling of a new domain of knowledge connex to the main them of the ontology - Philippe Rocca-Serra - ontology extension - - - - - - - - - an ontology extension process which happens on the fly, as users come up with the need. This is hard to accomplish as allowing user defined terms at will may lead to inconsistency and breakage. - Philippe Rocca-Serra - ontology dynamic extension - - - - - - - - - the process of formally describing a domain of knowledge - Philippe Rocca-Serra - knowledge representation - - - - - - - - - the process of breaking down a domain of knowledge according to rules - Philippe Rocca-Serra - knowledge formalization - - - - - - - - - the process of representing knowledge using formal rules, known as axiomsm, which allow automatic reasoning and solving - Philippe Rocca-Serra - axiomatic representation - - - - - - - - - the process of developing a domain representation by analysing data. - Philippe Rocca-Serra - data modeling - - - - - - - - - a data model is an information content entity which denotes and describes a domain of knowledge - Philippe Rocca-Serra - data model - - - - - - - - - the process of involving statistical methods, machine learning procedure to build a model which can be used to analysis new datasets and draw conclusions from never seen before data. - Philippe Rocca-Serra - model training - - - - - - - - - the process of classification is the process of identifying to which of a set of categories (sub-populations) a new observation belongs, on the basis of a training set of data containing observations (or instances) whose category membership is known - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/String-searching_algorithm - classification - - - - - - - - - data imputation is the process of replacing missing data with substituted values. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Imputation_(statistics) - data imputation - - - - - - - - - dealing with missing value is a process which aims to address the problems that occur when no data value is stored for the variable in an observation. Missing data are a common occurrence and can have a significant effect on the conclusions that can be drawn from the data. - Philippe Rocca-Serra - dealing with missing value - - - - - - - - - extract, transform, load (ETL) is the general procedure of copying data from one or more sources into a destination system which represents the data differently from the source(s) or in a different context than the source(s). - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Extract,_transform,_load - extract transform load process - - - - - - - - - the process of verifying that a data item supplied matches the specifications it is meant to comply with (e.g. an integer, a string,....) - Philippe Rocca-Serra - data type checking - - - - - - - - - the process of removing redundant entries which add volume without adding value - Philippe Rocca-Serra - duplicate removal - - - - - - - - - Philippe Rocca-Serra - pass through loading - - - - - - - - - the process of assessing the presence of a data item in a existing data strucuture or data storage system - Philippe Rocca-Serra - data lookup - - - - - - - - - the process of changing the encoding of information from one repertoir of characters convention (characterset) to another one - Philippe Rocca-Serra - characterset conversion - - - - - - - - - the process of changing the encoding of information from one convention to another one - Philippe Rocca-Serra - encoding conversion - - - - - - - - - the process of changing a numerical representation - Philippe Rocca-Serra - numerical conversion - - - - - - - - - the process of changing a date representation from one convention to another (e.g. from free to ISO8601) - Philippe Rocca-Serra - date conversion - - - - - - - - - the process of changing a numerical representation from one set of units to another one (e.g. from imperial to metric) - Philippe Rocca-Serra - unit conversion - - - - - - - - - the process of dividing the information contained in one element into at least 2 more components - Philippe Rocca-Serra - rule - field splitting - - - - - - - - - the process of bringing information from at least 2 components into one single element (e.g concatenation operation) - Philippe Rocca-Serra - rule - field merging - - - - - - - - - online analytical processing is the process which concerns itself with analyzing multidimensional data interactively from multiple perspectives. OLAP consists of three basic analytical operations: consolidation (roll-up), drill-down, and slicing and dicing - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Online_analytical_processing - olap operation - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube pivoting - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube slicing - - - - - - - - - a subtype of olap operation which ... - Philippe Rocca-Serra - data cube dicing - - - - - - - - - Data integrity is the maintenance of, and the assurance of the accuracy and consistency of, data over its entire life-cycle,[1] and is a critical aspect to the design, implementation and usage of any system which stores, processes, or retrieves data. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_integrity - data integrity checking - - - - - - - - - the process of computing a checksum of a digital document for the purpose of allowing data integrity checking during exchange and transmission - Philippe Rocca-Serra - file checksumming - - - - - - - - - the process of encoding digitical information to make it impossible to decipher without a key, known as the encryption key - Philippe Rocca-Serra - encryption - - - - - - - - - Data anonymization is a type of information sanitization whose intent is privacy protection. It is the process of either encrypting or removing personally identifiable information from data sets, so that the people whom the data describe remain anonymous. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_anonymization - anonymization - - - - - - - - - Pseudonymization is a data management and de-identification procedure by which personally identifiable information fields within a data record are replaced by one or more artificial identifiers, or pseudonyms. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Pseudonymization - pseudoanymization - - - - - - - - - Philippe Rocca-Serra - normalization - - - - - - - - - data mapping is the process of creating data element mappings between two distinct data models. Data mapping is used as a first step for a wide variety of data integration tasks, - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Data_mapping - mapping - - - - - - - - - the process of using software agent to perform a mapping task between data models - Philippe Rocca-Serra - automatic schema mapping - - - - - - - - - the process of using human expert to perform a mapping task between data models - Philippe Rocca-Serra - manual schema mapping - - - - - - - - - the process of using software agent to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - automatic ontology mapping - - - - - - - - - the process of using human expert to perform a mapping task between ontologies, semantic artefacts - Philippe Rocca-Serra - manual ology mapping - - - - - - - - - serialization (or serialisation) is the process of translating data structures or object state into a format that can be stored (for example, in a file or memory buffer) or transmitted (for example, across a network connection link) and reconstructed later (possibly in a different computer environment) - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Serialization - serialization - - - - - - - - - format conversion is a process on changing the representation model used during serialization - Philippe Rocca-Serra - format conversion - - - - - - - - - the process of checking and evaluating - Philippe Rocca-Serra - assessment - - - - - - - - - the process of checking against a set of rules and ensuring those are met - Philippe Rocca-Serra - validation - - - - - - - - - the process of checking against a set of rules which only concerns themselves with the grammar (syntax) but not the context. A syntactically valid document may contain incoherent content (semantic) - Philippe Rocca-Serra - syntactic validation - - - - - - - - - the process of checking against a set of semantic rules to ascertain information content validity (rather than its format) - Philippe Rocca-Serra - semantic validation - - - - - - - - - the process of checking against a set of constraints - Philippe Rocca-Serra - constraint validation - - - - - - - - - an assessment process which ascertain conformance to a set of specifications - Philippe Rocca-Serra - compliance assessment - - - - - - - - - the process of storing and serving data - Philippe Rocca-Serra - data hosting - - - - - - - - - the process of storing and serving files - Philippe Rocca-Serra - file hosting - - - - - - - - - the process of storing and serving semantic artefacts - Philippe Rocca-Serra - ontology hosting - - - - - - - - - the process of handling (minting, serving, deprecating, obsoleting) data item used to denotes and uniquely mark entities: - Philippe Rocca-Serra - identifier management - - - - - - - - - the process of creating an identifier (e.g. DOI) - Philippe Rocca-Serra - identifier minting - - - - - - - - - the process of handling a request formed from an identifier and direct the requesting agent to the relevant content - Philippe Rocca-Serra - identifier resolution - - - - - - - - - the process of provinding a correspondance between identifiers from 2 distinct resources for the equivalent entities - Philippe Rocca-Serra - identifier mapping - - - - - - - - - the process of leaving a marker in a location where a digital record has been withdrawn, in order to signify that the record had previously existed. - Philippe Rocca-Serra - identifier tombstoning - - - - - - - - - the process of preserving data and information in digital form - Philippe Rocca-Serra - data storage - - - - - - - - - a data storage process which uses a relational database management system - Philippe Rocca-Serra - rdbms data storage - - - - - - - - - a data storage process which uses a storage system indexing document directly - Philippe Rocca-Serra - document oriented data storage - - - - - - - - - a data storage process which stored data as a graph based representation (in contrast to table based representation as in RDBMS) - Philippe Rocca-Serra - graph data storage - - - - - - - - - the process of making a data object available to a public - Philippe Rocca-Serra - publication - - - - - - - - - the process of handling managing the evolution and changes to a data object - Philippe Rocca-Serra - versioning - - - - - - - - - an assessment process which focuses solely on data - Philippe Rocca-Serra - data assessment - - - - - - - - - an assessment process which relies on statistical methods and exploration to carry out an evaluation against a set of metrics - Philippe Rocca-Serra - statistical assessment - - - - - - - - - an assessment process carried by a human agent whose domain knowledge is recognized - Philippe Rocca-Serra - domain expert assessment - - - - - - - - - an assessment process carried by a group of human agent whose domain knowledge is recognized - Philippe Rocca-Serra - collegial/community assessment - - - - - - - - - a process which aims to evaluate the quality of an entity - Philippe Rocca-Serra - quality assessment - - - - - - - - - a process in which the delivery of a service or the quality of a product is assessed, and compared with that required. - Philippe Rocca-Serra - quality assurance - - - - - - - - - logical axiom is a rule defined in semantic model to allow for classification by automatic reasoners - Philippe Rocca-Serra - logical axiom - - - - - - - - - a rule which details the specific action which should be performed when a number of conditions are met - Philippe Rocca-Serra - functional rule - - - - - - - - - a rule which explains how to perform a specific curation action (for instance, a numeric conversion or a string replacement) - Philippe Rocca-Serra - curation rule - - - - - - - - - A regular expression, regex or regexp (sometimes called a rational expression) is a sequence of characters that define a search pattern. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Regular_expression - regular expression - - - - - - - - - a rule which explain how to relate one entity from a domain knowledge to another entity in another domain knowledge - Philippe Rocca-Serra - mapping rule - - - - - - - - - Philippe Rocca-Serra - metric - - - - - - - - - Philippe Rocca-Serra - quality metric - - - - - - - - - a textual entity associated with a semantic annotation in the form of an identifier corresponding to a term in an ontology - Philippe Rocca-Serra - ontology tagged entity - - - - - - - - - a textual entity which has been regularized through a curation process involving data transformation such as markup or substitution - Philippe Rocca-Serra - normalized textual entity - - - - - - - - - Philippe Rocca-Serra - file format - - - - - - - - - a file format specification whose rights are only available to the owner and creator of the said specifications - Philippe Rocca-Serra - propriatory file format - - - - - - - - - a file format whose specifications are available freely, with no restriction, allow full appraisal and review - Philippe Rocca-Serra - open file format - - - - - - - - - a file format which complies with a specification - Philippe Rocca-Serra - standard compliant file format - - - - - - - - - a data standard is a information content entity which prescribe syntax or semantic or both for a given domain knowledge - Philippe Rocca-Serra - Philippe Rocca-Serra - data standard - - - - - - - - - a standardized non-executable file type used by computer software as a pre-formatted example on which to base other files, especially documents - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Template_(file_format) - template - - - - - - - - - a template devised as a blueprint for operation such as extract transform load or similar data transformations - Philippe Rocca-Serra - Philippe Rocca-Serra - transformation template - - - - - - - - - a template devised for a regularized collection of annotation. - Philippe Rocca-Serra - Philippe Rocca-Serra - metadata acquisition template - - - - - - - - - a template devised for a regularized collection of annotated datasets - Philippe Rocca-Serra - data acquisition template - - - - - - - - - is a purpose-built database for the storage and retrieval of triples[1] through semantic queries. A triple is a data entity composed of subject-predicate-object, like "Bob is 35" or "Bob knows Fred". - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Triplestore - RDF triple store - - - - - - - - - knowledge model is an information content entity which corresponds to a representation of domain of human - Philippe Rocca-Serra - knowledge model - - - - - - - - - An entity‚Äìrelationship model (or ER model) describes interrelated things of interest in a specific domain of knowledge. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Conceptual_model#Data_models - object model - - - - - - - - - an object model following unified modeling language formalization - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Entity%E2%80%93relationship_model - uml model - - - - - - - - - Semantic data model is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Semantic_data_model - semantic data model - - - - - - - - - A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of sample data (and similar data from a larger population). A statistical model represents, often in considerably idealized form, the data-generating process. - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Statistical_model - statistical model - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - talend - - - - - - - - - a software service for performing curation services powered by machine learning techniques. - Philippe Rocca-Serra - tamr - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - trifacta - - - - - - - - - a software service for data curation and data cleanup provided by Google software company - Philippe Rocca-Serra - google refine - - - - - - - - - a software service for data storage and data mining provided by Google software company - Philippe Rocca-Serra - google bigtable - - - - - - - - - a software service for data curation and data cleaning provided by Amazon software company - Philippe Rocca-Serra - amazon comprehend - - - - - - - - - a software service for data storage and data mining provided by Amazon software company - Philippe Rocca-Serra - amazon redshift - - - - - - - - - a software service for data storage and data mining provided by Microsoft software company and the Azure cloud solution - Philippe Rocca-Serra - microsoft azure - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - tableau - - - - - - - - - a software service for performing ETL operations provided by software company Pentaho, a subsidiary of Hitachi. - Philippe Rocca-Serra - penthaho kettle - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - sisense - - - - - - - - - a software suite for business intelligence, data wrangling and data mining - Philippe Rocca-Serra - elsevier - - - - - - - - - a software service which offers support for semantic and knowledge management - Philippe Rocca-Serra - poolparty - - - - - - - - - a software service provided by SciBite company to manage controlled terminologies and curation function, combining functions equivalent to OLS,zooma and oxo - Philippe Rocca-Serra - centinel - - - - - - - - - a software service provided by EMBL-EBI SOFT group, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ontology lookup service - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which assist curation based on prior of existing curated and annotated dataset from ArrayExpress database - Philippe Rocca-Serra - zooma - - - - - - - - - a software service provided bu EMBL-EBI SOFT group which serves mapping between ontologies - Philippe Rocca-Serra - oxo - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies, which serves controled terminologies, allowing searches and exploration and term selection. - Philippe Rocca-Serra - ncbo bioportal - - - - - - - - - a software service provided by the National Center for Biomedical Ontologies which, given a body of text and a set of ontologies will return annotation hits. - Philippe Rocca-Serra - ncbo annotator - - - - - - - - - a process of choosing or granting a license to an entity (software, hardware,data) - licensing - - - - - - - - - a process which aim to ensure continuation, persistance of a service or structure at minima to maintain its existence and availability. - Philippe Rocca-Serra - maintenance - - - - - - - - - a process which defines how means are assigned to people or organization to execute a task - Philippe Rocca-Serra - resource allocation - - - - - - - - - Philippe Rocca-Serra - team organization - - - - - - - - - a process which consists in estimating the performance of a process based on value addition generated by said process - Philippe Rocca-Serra - value based assessment - - - - - - - - - a rule deterrmine who, when, what and how entities may be made available. - Philippe Rocca-Serra - access condition - - - - - - - - - an access protocol is a software specification defining the implementation for obtaining data under a number of access conditions - Philippe Rocca-Serra - access protocol - - - - - - - - - file transfer protocol is a standard network protocol used for the transfer of computer files between a client and server on a computer network. FTP specifications evolved from the initial RFC114 from 1971 to the latest specification RFC2428 adding support for IPv6 in 1998. - Wikipedia - ftp - - - - - - - - - The Hypertext Transfer Protocol (HTTP) is an application protocol for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web. It is an international standard specified by RFC 2068 in 1997 (HTTP1.1), obsoleted by RFC 2616 in 1999, which was likewise replaced by the RFC 7230 family of RFCs in 2014. - Wikipedia - http - - - - - - - - - secure file transfer protocol is a secured version of the FTP procotol, which relies on SSH authentication - Wikipedia - sftp - - - - - - - - - An application programming interface (API) is a computing interface which defines interactions between multiple software intermediaries - Wikipedia - application programming interface - - - - - - - - - Representational state transfer (REST) is a software architectural style that defines a set of constraints to be used for creating Web services, introduced and defined in 2000 by Roy Fielding in his doctoral dissertation. HTTP-based RESTful APIs are defined with the following aspects: - --a base URI, such as http://api.example.com/collection/; --standard HTTP methods (e.g., GET, POST, PUT, PATCH and DELETE); --a media type that defines state transition data elements - Philippe Rocca-Serra - rest api - - - - - - - - - SOAP (abbreviation for Simple Object Access Protocol) is a messaging protocol specification for exchanging structured information in the implementation of web services in computer networks. Its purpose is to provide extensibility, neutrality, verbosity and independence.[vague] It uses XML Information Set for its message format, and relies on application layer protocols, most often Hypertext Transfer Protocol (HTTP), although some legacy systems communicate over Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission - Wikipedia - soap api - - - - - - - - - The OpenAPI Specification, originally known as the Swagger Specification, is a specification for machine-readable interface files for describing, producing, consuming, and visualizing RESTful web services. - Wikipedia - open/smart api - - - - - - - - - an API which is built using the GraphQL is a query language, a specification, and a set of tools that operates over a single endpoint using HTTP. It is meant to address the issue of "over and under fetching" during querying REST endpoints. GraphQL language was developed by Facebook. (https://www.howtographql.com/basics/1-graphql-is-the-better-rest/) - Philippe Rocca-Serra - graphql api - - - - - - - - - a quality to indicate the stage at which an entity is in its life cycle - Philippe Rocca-Serra - maturity level - - - - - - - - - a maturity level with indicates an early phase, for feasability study capability - Philippe Rocca-Serra - exploratory - - - - - - - - - a maturity level with indicates an early phase, for evaluation and testing assessment capability - Philippe Rocca-Serra - prototypic - - - - - - - - - a maturity level which indicates developing capability which has not reached full potential - Philippe Rocca-Serra - immature - - - - - - - - - a maturity level which indicates a stable, fully fledged capability - Philippe Rocca-Serra - mature - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment capability - Philippe Rocca-Serra - production grade - - - - - - - - - a maturity level which indicates a reference status for a capability in its domain. - Philippe Rocca-Serra - state of the art - - - - - - - - - a maturity level which indicates a stable, susceptible to be deployed in production environment - Philippe Rocca-Serra - deployed - - - - - - - - - a maturity level which indicates declining capability - Philippe Rocca-Serra - obsolescent - - - - - - - - - a maturity level which indicates a capability has reached the end of its life. - Philippe Rocca-Serra - obsolete - - - - - - - - - a maturity level which indicates a capability has been removed from frontline production. - Philippe Rocca-Serra - retired - - - - - - - - - Data is managed as a requirement to support the analytical workflows of the project, focused on delivering its own results' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_1 - - - - - - - - - Data is managed as a critical research data asset. Achieve a level of management that enables project to efficiently use and manipulate its data assets' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_2 - - - - - - - - - Data is managed according to community standards with re-usability beyond the project scope in mind' - https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_3 - - - - - - - - - Usability and Applicability of Data for use and re-use is measured against metrics to evaluate the implemented processes of the data management environment' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_4 - - - - - - - - - The Environment processes are considered community best practices for FAIR data management' - Defined in https://docs.google.com/presentation/d/1nq9KDHPDSsQnT3UyLGOXSDsEgDz88WYZyBTKnugwph8/edit#slide=id.p20' - Maturity_Level_5 - - - - - - - - - a quality to indicate the size of the grain in the physical world. by abstraction, a quality to indicate how atomic an entity is. - granularity level - - - - - - - - - a quality to indicate a small size of the entities making up an assembly. - fine - - - - - - - - - a quality to indicate a lack of refinement of the entities making up an assembly. - coarse - - - - - - - - - a quality to indicate the medium size of the entities making up an assembly. - intermediate - - - - - - - - - a quality to indicate how easy or hard it is to locate/find an entity - findability - - - - - - - - - a quality to indicate that an information entity is indexed by global search engines such as Bing,Google,Yandex,DuckDuckGo..) - search engine referenced - - - - - - - - - a quality to indicate that an information entity is markup with schema.org ontology terms - schema.org annotated - - - - - - - - - a quality to indicate that an information entity is available from a data archive - deposited in public archive - - - - - - - - - a quality to indicate that an information entity is available from a data archive and has been assigned a persistent url - assigned with a persistent http resolveable identifier - - - - - - - - - a quality to indicate that an information entity metadata is conformant to datacite metadata schema and has been assigned a Digital Object Identifier (DOI) - doi-ed - - - - - - - - - a quality to indicate how easy or hard it is to understand how an entity may be access and then access it - accessibility - - - - - - - - - a quality to indicate that no access to the entity is possible other than physical site visit - enclaved - - - - - - - - - a quality to indicate that the entity can only be accessed provided the necessary amount of credentials and authorization - access-controlled - - - - - - - - - a quality to indicate how systems are capable of interacting and working together automatically - interoperability - - - - - - - - - a quality which indicates the entity is conformant to an information specification - standard compliant - - - - - - - - - a quality which indicates the entity is conformant to an information specification as assessed by a certification body - standard certified - - - - - - - - - a quality to indicate how easy or hard it is to mobilize and reuse an information entity , for instance in the context of meta-analysis and data integration. - reusability - - - - - - - - - a role to manage company/organization data to ensure security of electronic information related to the organisation and implement systems to offer efficient analysis, storage and documentation of company records. Reduce costs by identifying bad data practices and replacing them with improved practices. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957283 - data manager - - - - - - - - - a data steward is a role within an organization responsible for utilizing an organization's data governance processes to ensure fitness of data elements - both the content and metadata. - https://en.wikipedia.org/wiki/Data_steward - data steward - - - - - - - - - the role of a personel in charge of performing computational or statistical analysis over company/organisation digital assets and datasets - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957285 - data analyst - - - - - - - - - A data custodian ensures that 1) Access to the data is authorized and controlled. 2)Data stewards are identified for each data set. 3)Technical processes sustain data integrity. 4)Processes exist for data quality issue resolution in partnership with Data Stewards. 5)Technical controls safeguard data. 6)Data added to data sets are consistent with the common data model. 7)Versions of Master Data are maintained along with the history of changes. 8)Change management practices are applied in maintenance of the database. 9)Data content and changes can be audited - https://en.wikipedia.org/wiki/Data_custodian - data custodian - - - - - - - - - the role of a personal to bring expertice and knowledge in a specific domain - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957287 - subject matter export - - - - - - - - - the role of a personel in an organization/company to organization, oversee and decide on all tasks related to data and information management in said organization. The role involves taking executive decisions. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957288 - chief information officer - - - - - - - - - the role of a personel in an organization/company to perform and carry out scientific research - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957289 - scientist/researcher - - - - - - - - - the role of a personel in an organization/company in charge of performing data analysis and research with data, around data and about data to deliver scientific insight to the decision makers. - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957290 - data scientist - - - - - - - - - the role of a personel in an organization/company with the power of taking executive decisions - https://docs.google.com/spreadsheets/d/1l_l3Zecd-O0fMv_8DTTKjznDuxbqEdtTVMhR9fyK7SM/edit#gid=1264957291 - decision maker - - - - - - - - - the role of an organization to deliver information technology services. - IT provider - - - - - - - - - the role of a personel in an organization to operate on data once clearance has been obtained from a data controller or data custodian - data processor - - - - - - - - - the role of a personel to supervise, organize and manage protection and privacy of data. - https://ec.europa.eu/info/law/law-topic/data-protection/reform/rules-business-and-organisations/obligations/controller-processor/what-data-controller-or-data-processor_en - data controller - - - - - - - - - the role of a personel to conceive information technology solution and computer code in the form of deployable software. - software engineer - - - - - - - - - the role of a personel to preserve, annotate, archive digital assets produced or purchased by an organization. - data curator - - - - - - - - - a plan documenting the resources and practices, such as ontologies, data formats, information standards and backup, protection measures respectively with the objective of ensuring proper data management. - data management plan - - - - - - - - - a document outlining the semantic resources, terminologies, controlled vocabularies and data format against which curation will be applied. Such document. also specifies the steps requires to version datasets following curation action. - curation policy - - - - - - - - - a data dictionnary is a document listing all the variables and their values sets for categorical variables or numerical ranges of values for continuous values, as well as associated units, formulas for computed derived variables, codes and rules for dealing with missing value. - data dictionary - - - - - - - - - a material transfer agreement (MTA) is a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document. - Wikipedia - material transfer agreement - - - - - - - - - a data access agreement (DAA) is a document to specify the terms under which users are provided access to the specified data, and to obtain explicit acceptance of those terms by a user prior to granting him or her access to the data. It is usually legally binding and requires legal representatives of said organizations to supervised the writing and approval of the document - data access agreement - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - - obsolete_core - true - - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - A reference to a place on the Earth, by its name or by its geographical location. - geographic location - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -