diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 2dbf92b..d17e4d2 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4.3 + container: obolibrary/odkfull:v1.5.1 # Steps represent a sequence of tasks that will be executed as part of the job steps: @@ -29,5 +29,5 @@ jobs: - name: Run ontology QC checks env: DEFAULT_BRANCH: main - run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false diff --git a/RIDDLE-base.owl b/RIDDLE-base.owl index d4ff9ab..acb2b84 100644 --- a/RIDDLE-base.owl +++ b/RIDDLE-base.owl @@ -9,12 +9,12 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:dcterms="http://purl.org/dc/terms/"> - + - None + Ontology for project RIDDLE - RIDDLE project ontology - 2023-10-12 + Mortality Prediction for Hospitalized Patient Ontology + 2024-08-02 @@ -38,47 +38,22 @@ - - description - + - - license - + - - title - - - - - - - - - - - - - root node - + - + diff --git a/RIDDLE-full.owl b/RIDDLE-full.owl index 9444d7a..823c5c5 100644 --- a/RIDDLE-full.owl +++ b/RIDDLE-full.owl @@ -7,24 +7,22 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:HOSO="http://purl.obolibrary.org/obo/HOSO.owl#" - xmlns:IOIO="http://purl.obolibrary.org/obo/IOIO#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:HEPRO="http://purl.obolibrary.org/obo/HEPRO#" - xmlns:HOSO1="http://purl.obolibrary.org/obo/HOSO#" + xmlns:MPHPO="http://purl.obolibrary.org/obo/MPHPO#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:OpenLHS-Core="http://purl.obolibrary.org/obo/OpenLHS-Core#" xmlns:CommonCoreOntologies="http://www.ontologyrepository.com/CommonCoreOntologies/"> - - None + + Ontology for project RIDDLE - RIDDLE project ontology - 2023-10-12 + Mortality Prediction for Hospitalized Patient Ontology + 2024-08-02 @@ -301,38 +299,21 @@ - + - - HEPRO-H + + Subset for RIDDLE project + MPHPO-Slim - + - - HOSO classes relevant to humans. - HOSO-H - - - - - - - - - - - - - - - - - IOIO classes relevent to humans. - IOIO-H + + OpenLHS classes relevant to humans. + OpenLHS-H @@ -460,6 +441,25 @@ + + + + + + + + + ISO8601 DateTime + + + + + + + + + + + + + has textual representation + + + + + + + + + has value + + + + + + + + + has numerical value + + + + + + + + + has temporal value + + + + + + + + + has text value + + + + - + @@ -3280,7 +3338,8 @@ every c that is a concretization of g specifically denotes r An individual identifier that denotes a health provider. - + + health provider identifier @@ -3290,8 +3349,15 @@ every c that is a concretization of g specifically denotes r + + + + 1 + + + A health provider identifier that is used to denote a person authorised to act as a physician. - + physician identifier @@ -3310,7 +3376,7 @@ every c that is a concretization of g specifically denotes r A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities. This usually includes health professional like physicians, nurses or pharmacists etc. It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants. - + health provider role @@ -3319,7 +3385,7 @@ It could also includes non professionals like patient attendant but it would exc - + @@ -3327,7 +3393,8 @@ It could also includes non professionals like patient attendant but it would exc An organism that is the bearer of a health provider role. - + + health provider @@ -3337,8 +3404,8 @@ It could also includes non professionals like patient attendant but it would exc - TBD - + A health procedure that include a diagnostic procedure - TBD. + diagnostic health procedure @@ -3348,8 +3415,8 @@ It could also includes non professionals like patient attendant but it would exc - TBD - + A health procedure that includes a surgical procedure - TBD. + surgical health procedure @@ -3524,6 +3591,7 @@ It could also includes non professionals like patient attendant but it would exc A directive information entity that aims to direct a health procedure. A directive information entity that aims to direct a health procedure. + health procedure specification @@ -3685,6 +3753,7 @@ It could also includes non professionals like patient attendant but it would exc A service agreement specification identifying an organism for whom a healthcare service delivery aims at providing a desired effect to its health status. + healthcare service organism specification @@ -3694,7 +3763,7 @@ It could also includes non professionals like patient attendant but it would exc - TBD + A facility that bears a healthcare function - WiP. healthcare facility @@ -3748,6 +3817,7 @@ It could also includes non professionals like patient attendant but it would exc A health provider who is a member of a healthcare organisation. + healthcare provider @@ -3780,7 +3850,8 @@ It could also includes non professionals like patient attendant but it would exc A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization. - + + healthcare organization service delivery @@ -3799,7 +3870,13 @@ It could also includes non professionals like patient attendant but it would exc - + + + + + + + @@ -3810,7 +3887,8 @@ It could also includes non professionals like patient attendant but it would exc A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes. - + + healthcare organization clinical visit @@ -3821,7 +3899,7 @@ It could also includes non professionals like patient attendant but it would exc A service delivery that aims to support health services without directly providing a desired effect on the health status of individuals or communities. - + ancillary care service delivery @@ -3832,7 +3910,7 @@ It could also includes non professionals like patient attendant but it would exc A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities. - + custodial care service delivery @@ -3843,7 +3921,7 @@ It could also includes non professionals like patient attendant but it would exc A healthcare service that aims at providing a desired effect on the health status of a community. - + populational healthcare service @@ -3854,7 +3932,7 @@ It could also includes non professionals like patient attendant but it would exc A temporally-connected healthcare organization clinical visit that aims to improve, maintain or restore the health of some participating organism. - + healthcare organization clinical encounter @@ -3877,7 +3955,7 @@ It could also includes non professionals like patient attendant but it would exc A healthcare encounter during which the recipient is located in a healthcare facility at some time. - + facility-supported healthcare encounter @@ -3887,6 +3965,7 @@ It could also includes non professionals like patient attendant but it would exc + @@ -3894,7 +3973,7 @@ It could also includes non professionals like patient attendant but it would exc An identifier that denotes a public provincial health insurance record. - + public provincial health identifier @@ -3932,7 +4011,7 @@ It could also includes non professionals like patient attendant but it would exc A healthcare organisation clinical visit where the patient physically attends to a healthcare facility, but where there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient. - + outpatient visit @@ -3949,7 +4028,7 @@ It could also includes non professionals like patient attendant but it would exc A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient. - + inpatient visit @@ -3960,7 +4039,7 @@ It could also includes non professionals like patient attendant but it would exc An inpatient visit that does not extend overnight. - + day inpatient visit @@ -3977,7 +4056,7 @@ It could also includes non professionals like patient attendant but it would exc A day inpatient visit which includes a surgical procedure. - + day inpatient surgery visit @@ -3988,7 +4067,8 @@ It could also includes non professionals like patient attendant but it would exc An inpatient visit located in a hospital facility requested by a physician, that may extends overnight. - + + hospitalization @@ -4000,7 +4080,8 @@ It could also includes non professionals like patient attendant but it would exc A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. It is not necessarily an immediate inpatient subsequent visit. - + + emergency department visit @@ -4020,7 +4101,7 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit and an inpatient visit, where there is usually limited accommodation and where the goal is to stabilise a life-threatening condition or decide whether the clinical situation requires a hospitalisation visit. - + emergency department inpatient visit @@ -4040,8 +4121,8 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit and an outpatient visit. - there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient - + There is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient + emergency department outpatient visit @@ -4051,8 +4132,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions - + An outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions. + walk-in clinic visit @@ -4068,8 +4149,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit which includes a surgical procedure - + An outpatient visit which includes a surgical procedure. + outpatient surgery visit @@ -4085,8 +4166,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit which includes a diagnostic procedure - + An outpatient visit which includes a diagnostic procedure. + outpatient diagnostic visit @@ -4106,7 +4187,7 @@ It is not necessarily an immediate inpatient subsequent visit. An immediate subsequent visit healthcare organisation visit for a given patient that was participating in another healthcare organisation visit for the same organisation just prior to this visit. - + immediate inpatient subsequent visit @@ -4133,7 +4214,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity describing the type of visit that occured prior to an immediate inpatient subsequent visit. - + prior visit category to an inpatient visit @@ -4144,7 +4225,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organisation service delivery where the main entity of interest is a still born. - + still born healthcare service @@ -4195,7 +4276,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization clinical visit during which a birth statement was produced regarding the birth of the main patient visit beneficiary. In the case of human health the specified organism refers to the child born during the visit. - + healthcare birth visit @@ -4208,7 +4289,7 @@ It is not necessarily an immediate inpatient subsequent visit. Patient hospitalized directly from home. Patient transferred from a healthcare organization emergency department to be hospitalized by a different healthcare organization. an inpatient visit that is not immedately following another healthcare organisation clinical visit in the same organisation, and is not a healthcare birth visit - + inpatient visit from an external location @@ -4217,10 +4298,29 @@ It is not necessarily an immediate inpatient subsequent visit. + + + + + + + + + + + + + + + + + An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. - + Considérer axomatisation séquentielle + + ambulance initiated emergency department visit @@ -4231,7 +4331,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization service delivery where the main entity of interest is a human cadaver that was not delivered just prior to this service. - + cadaver service @@ -4282,7 +4382,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization clinical visit during which a death statement was produced regarding the death of the main patient visit beneficiary. A healthcare organization clinical visit during which the patient died. - + healthcare visit of expiration @@ -4299,7 +4399,7 @@ It is not necessarily an immediate inpatient subsequent visit. A directive information entity that aims at directing what health procedures or healthcare organization services are recommended after this visit. - + visit discharge specification @@ -4316,7 +4416,7 @@ It is not necessarily an immediate inpatient subsequent visit. A visit discharge specification that aims at directing to which healthcare organisation the patient should be transferred after the end of the current visit. - + visit transfer specification @@ -4333,7 +4433,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that is part of a visit transfer specification and is about the type of healthcare organization specified. - + visit transfer specification category @@ -4359,7 +4459,7 @@ It is not necessarily an immediate inpatient subsequent visit. A visit discharge specification for a given clinical visit that has no visit transfer specification. - + visit discharge specification for home @@ -4385,7 +4485,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization clinical visit ended at the initiative of the patient without physician approval. - + visit ended by the patient @@ -4396,7 +4496,7 @@ It is not necessarily an immediate inpatient subsequent visit. A visit ended by the patient without notifying the healthcare organization. - + visit ended by the patient without notification @@ -4407,7 +4507,7 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit with a triage encounter but no further encounter. - + triage-only emergency department visit @@ -4419,7 +4519,7 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit and a visit ended by the patient and some treatment healthcare procedure was provided. - + emergency department visit with partial treatment @@ -4431,7 +4531,7 @@ It is not necessarily an immediate inpatient subsequent visit. An identifier that denotes a diagnosis related group. DRG code - + visit diagnosis related group code @@ -4455,7 +4555,8 @@ It is not necessarily an immediate inpatient subsequent visit. A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. - + + healthcare organization service delivery beginning statement @@ -4479,7 +4580,8 @@ It is not necessarily an immediate inpatient subsequent visit. A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. - + + healthcare organization service delivery ending statement @@ -4497,7 +4599,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that contains the information required to manage the insurance coverage of an insured individual. - + public provincial health insurance record @@ -4600,7 +4702,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization clinical visit for a given patient that was participating in another healthcare organisation clinical visit just prior to this visit. - + immediate subsequent visit @@ -4611,18 +4713,267 @@ It is not necessarily an immediate inpatient subsequent visit. An immediate subsequent visit where both visits are under the responsability of the same healthcare organisation. - + immediate subsequent visit in same organization + + + + + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + direct ambulance initiated hospitalization + + + + + + + + + A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider. + + ambulance paramedics visit + + + + + + + + + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit. + + ED by ambulance initiated hospitalization + + + + + + + + + A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit. + ICU admission specification + + + + + + + + + A service agreement specification for a clinical visit admission. + clinical visit agreement specification + + + + + + + + + A clinical visit agreement specification mandating the urgency level of the clinical visit. + clinical visit urgency level specification + + + + + + + + + A clinical visit urgency level specification mandating the urgency level of the hospitalization admission. + hospitalization admission urgency level specification + + + + + + + + + A clinical visit agreement specification mandating the type of unit required for a clinical visit. + clinical visit unit type specification + + + + + + + + + + + + + + + A clinical visit agreement specification mandating the admitting physician. + hospitalization admitting physician specification + + + + + + + + + + + + + + + A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members + It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department. + It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon). + healthcare physician service + + + + + + + + + + + + + + + + + + + + + A primary residence statement that states the type of living environment of a patient immediately prior to a clinical visit. + living environment type prior to clinical visit statement + + + + + + + + + + + + + + + An eukaryote that is the bearer of a patient role. + patient + + + + + + + + + + + + + + + A role born by an organism which is the primary recipient in a healthcare organization clinical visit. + patient role + + + + + + + + + + + + + + + + + + A patient that is a Homo sapiens. + human patient + + + + + + + + + + + + 1 + + + + A healthcare organization identifier that denotes a physician service. + healthcare physician service identifier + + + + + + + + + + An identifier that denotes a healthcare organization service delivery. An identifier that denotes a healthcare organization service delivery. + healthcare organization service delivery identifier @@ -4632,6 +4983,12 @@ It is not necessarily an immediate inpatient subsequent visit. + + + + + + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. healthcare organization service delivery beginning temporal information @@ -4698,6 +5055,12 @@ It is not necessarily an immediate inpatient subsequent visit. + + + + + + @@ -4759,6 +5122,7 @@ It is not necessarily an immediate inpatient subsequent visit. + human clinical visit specified patient @@ -4787,7 +5151,8 @@ It is not necessarily an immediate inpatient subsequent visit. An identifier that denotes a healthcare provider. - + + healthcare provider identifier @@ -4814,7 +5179,7 @@ It is not necessarily an immediate inpatient subsequent visit. - + facility-supported clinical visit @@ -4866,7 +5231,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that aims at representing the various forms of care provided within the healthcare organization clinical visit as approximated by a case-mix group definition. DRG - + diagnosis related group @@ -5337,7 +5702,7 @@ When there is no such string, it is almost always because the entities take the Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. - + human birth statement @@ -5358,7 +5723,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 A state sanctioned human birth statement. A state sanctioned human birth statement. - + civil birth record @@ -5383,7 +5748,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965Reese, Kyle died in 1984 A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. - + human death statement @@ -5404,7 +5769,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 A state sanctioned human death statement. A state sanctioned human death statement. - + civil death record @@ -5462,7 +5827,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 A biological sex information content entity that denotes the biological sex of a human. A biological sex information content entity that denotes the biological sex of a human. - + human biological sex information content entity @@ -5482,7 +5847,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 An information content entity that denotes a biological sex or a gender identity of a human. An information content entity that denotes a biological sex or a gender identity of a human. - + human biological sex or gender identity information content entity @@ -5513,6 +5878,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965'Goose' (the name of a cat) An identifier that denotes a particular organism. An identifier that denotes a particular organism. + organism identifier @@ -5542,7 +5908,8 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 An organism identifier that denotes a particular human. An organism identifier that denotes a particular human. - + + human identifier @@ -5551,7 +5918,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - + @@ -5564,8 +5931,9 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - A statement stating the biological sex of a human. - A statement stating the biological sex of a human. + A pragmatically accepted statement stating the biological sex of a human. + A pragmatically accepted statement stating the biological sex of a human. + human biological sex statement @@ -5593,6 +5961,206 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 + + + + A pragmatically accepted statement that states characteristics of the primary residence of an individual at a given moment in time. + primary residence statement + + + + + + + + + An information content entity that aims at representing a type of living environment applicable to a primary residence. + living environment type + + + + + + + + + + + + 1 + + + + + Human birth date with data property + MPHPO human birth date + + + + + + + + + + + + 1 + + + + + human biological sex ICE with data property + MPHPO human biological sex information content entity + + + + + + + + + + + + 1 + + + + + ICU admission specification with data property + MPHPO ICU admission specification + + + + + + + + + + + + 1 + + + + + hospitalization admission urgency level specification with data property + MPHPO hospitalization admission urgency level specification + + + + + + + + + + + + 1 + + + + + healthcare physician service identifier with data property + MPHPO healthcare physician service identifier + + + + + + + + + + + + 1 + + + + + pathological condition impact type on clinical visit with data property + MPHPO pathological condition impact type on clinical visit + + + + + + + + + + + + 1 + + + + + pathological condition sub-group name with data property + MPHPO pathological condition sub-group name + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery beginning temporal information with data property + MPHPO healthcare organization service delivery beginning temporal information + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery ending temporal information with data property + MPHPO healthcare organization service delivery ending temporal information + + + + + + + + + + + + 1 + + + + + living environment type with data property + MPHPO living environment type + + + + @@ -5648,6 +6216,8 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965human human being + + Homo sapiens @@ -5692,6 +6262,7 @@ objectives is a planned process. 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + planned process @@ -5952,7 +6523,7 @@ edited date: 30 SEPT 2015 - + @@ -5963,14 +6534,14 @@ edited date: 30 SEPT 2015 Mathias Brochhausen facility - + - + 09/09/2017 @@ -6604,6 +7175,70 @@ edited date: 30 SEPT 2015 + + + + + + + + 1 + + + 4 Km + An information content entity whose structure and content follow a template. + specified value + + + + + + + + + numerical specified value + + + + + + + + + + + + 1 + + + + + + + 1 + + + + unit qualified scalar specified value + + + + + + + + + + + + + + + unit + + + + @@ -6648,19 +7283,12 @@ edited date: 30 SEPT 2015 An information content entity that denotes a one-dimension temporal region. An information content entity that denotes a one-dimension temporal region. + temporal information - - - - root node - - - - @@ -7008,5 +7636,5 @@ The phrase "the pink elephant" describes an entity, but is not a &apos - + diff --git a/RIDDLE-non-classified.owl b/RIDDLE-non-classified.owl new file mode 100644 index 0000000..1e834ad --- /dev/null +++ b/RIDDLE-non-classified.owl @@ -0,0 +1,7459 @@ + + + + + Ontology for project RIDDLE + + Mortality Prediction for Hospitalized Patient Ontology + 2024-08-02 + + + + + + + + + + + + + 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 + + + + + + + + + example of usage + + + + + + + + + + + + + + + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + curator note + + + + + + + + + + + + + + + imported from + + + + + + + + + elucidation + + + + + + + + + has associated axiom(nl) + + + + + + + + + has associated axiom(fol) + + + + + + + + + has axiom label + + + + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary conditions + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary conditions associated with an entity, we write as definitional necessary condition the conjunction of them. + + + + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary and sufficient conditions + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary and sufficient conditions associated with an entity, we regroup them in the same annotation. + + + + + + + + Human-readable necessary membership condition(s) of a class or a property. + We introduce 'necessary conditions' rather than 'necessary condition' to avoid the multiplication of annotations. + necessary conditions + + + + + + + + Human-readable necessary and sufficient membership conditions of a class or a property. + necessary and sufficient conditions + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subset for RIDDLE project + MPHPO-Slim + + + + + + + + + OpenLHS classes relevant to humans. + OpenLHS-H + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ISO8601 DateTime + + + + + + + + + + + + + + + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 + + + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + TBD + has participating performer + + + + + + + + + TBD + has participating recipient + + + + + + + + + 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 + + + + + + + + Inverse of the relation 'mentions' + + + 2022-01-28T07:20:08Z + mentioned by + + + + + + + + + + + + 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 + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + The inverse property of is_specified_input_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 + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + 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. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + The inverse property of is_specified_output_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 + + + + + + + + + is administered by + + + + + + + + + + + + + A relation that holds between a filler and a slot it fills. + fills + + + + + + + + + + + The inverse relations of directs + The inverse relations of directs + is directed by + + + + + + + + + + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + is about an aspect of + + + + + + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + A directs B := A is a directive information entity that guides an agent in the execution of B. + directs + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + This includes failed attempts where B is not compliant to A. + + + + + + + + + + + + The inverse relation of fills + The inverse relation of fills + is filled by + + + + + + + + + + + A maximally directs B := A directs B, and B is compliant to A. + A maximally directs B := A directs B, and B is compliant to A. + Discussed in: Adrien Barton, Laure Vieu, Jean-François Ethier. Directing Actions. Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), Sep 2019, Graz, Austria. + maximally directs + + + + + + + + + + + The inverse relation of maximally directs. + The inverse relation of maximally directs. + is maximally directed by + + + + + + + + + + The inverse relation of has component. + The inverse relation of has component. + component of + + + + + + + + + + + + The inverse relation of has component process. + The inverse relation of has component process. + component process of + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic + + + + + + + + + + + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + + 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 + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + + x agent_in y iff y is an instance of Process and x is an instance of Agent, such that x is causally active in y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + agent in + + + + + + + + + + + + + + + + + + + + x has_agent y iff x is an instance of Process and y is an instance of Agent, such that y is causally active in x. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has agent + + + + + + + + + + + x has_capability y iff x is an instance of Agent and y is an instance of Agent Capability, such that x bearer of y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has capability + + + + + + + + + + + + + + has textual representation + + + + + + + + + has value + + + + + + + + + has numerical value + + + + + + + + + has temporal value + + + + + + + + + has text value + + + + + + + + + + + + + + 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 + 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 + 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 + 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] + + + + + + + + + + + + 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 + + + + + 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 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] + + + + + + + + + + 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. + 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 + + + + + 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 + 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 + + + + + (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] + + + + + + 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] + + + + + + + + + + + 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 + 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 + 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. + 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 + + + + + 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. + 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 + 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 + + + + + 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]) + + + + + + + + + + + + + + + + A request requesting the execution of some health procedure. + A request that has as part a health procedure specification. + A request requesting the execution of some health procedure. + + health procedure request + + + + + + + + + An information content entity containing information about some health procedure requests and possibly the associated health procedures. + + health procedure report + + + + + + + + + + + + + + + + + + + + + + + + + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + A planned process that has some components that are planned processes, including at least one that is a health activity. + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + + + health procedure + + + + + + + + + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + + health activity + + + + + + + + + + + + + + + A planned process that is a part of a health procedure, that has as specified input at least one health activity outcome information and aim at generating a health procedure outcome information. + + health procedure resulting process + + + + + + + + + + + + + + + An information content entity that is the output of a health procedure resulting process and that describes some outcomes of a health procedure. + + health procedure outcome information + + + + + + + + + + + + + + + An information content entity that is a specified output of a health activity. + An information content entity that is a specified output of a health activity. + + health activity outcome information + + + + + + + + + + + + 1 + + + + An individual identifier that denotes a health provider. + + + health provider identifier + + + + + + + + + + + + 1 + + + + A health provider identifier that is used to denote a person authorised to act as a physician. + + physician identifier + + + + + + + + + + + + + + + A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities. + This usually includes health professional like physicians, nurses or pharmacists etc. +It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants. + + health provider role + + + + + + + + + + + + + + + An organism that is the bearer of a health provider role. + + + health provider + + + + + + + + + A health procedure that include a diagnostic procedure - TBD. + + diagnostic health procedure + + + + + + + + + A health procedure that includes a surgical procedure - TBD. + + surgical health procedure + + + + + + + + + + + + + + + 'curative procedures' +'Surgeries performed on June, 19th 2023 at Velpeau Hospital' + An information content entity that is about a sub-group of health procedures. + We suppose that if an ICE is about a group of particular entities, it is also about each of these entities. + health procedure sub-group name + + + + + + + + + + + + + + + 'laboratory test' + An information content entity that is about a sub-group of health activities. + We suppose that if an ICE is about a group of particular entities, it is also about each of these entities. + health activity sub-group name + + + + + + + + + + + + + + + An information content entity that is about a sub-group of pathological conditions. + We suppose that if an ICE is about a group of particular entities, it is also about each of these entities. + pathological condition sub-group name + + + + + + + + + + + + + + + + + + + + + A process beginning statement that temporally qualifies the beginning of a health procedure. + A process beginning statement that temporally qualifies the beginning of a health procedure. + health procedure beginning statement + + + + + + + + + + + + + + + + + + + + + A process ending statement that temporally qualifies the end of a health procedure. + health procedure ending statement + + + + + + + + + + + + + + + + + + + + + A process beginning statement that temporally qualifies the beginning of a health activity. + A process beginning statement that temporally qualifies the beginning of a health activity. + health activity beginning statement + + + + + + + + + + + + + + + + + + + + + A process ending statement that temporally qualifies the end of a health activity. + A process ending statement that temporally qualifies the end of a health activity. + health activity ending statement + + + + + + + + + + + + + + + A service agreement specification that aims to direct some health procedure. + A service agreement specification that has as part a health procedure specification. + A service agreement specification that aims to direct some health procedure. + health procedure agreement specification + + + + + + + + + A directive information entity that aims to direct a health procedure. + A directive information entity that aims to direct a health procedure. + + health procedure specification + + + + + + + + + An identifier that denotes a health activity. + An identifier that denotes a health activity. + health activity identifier + + + + + + + + + An identifier that denotes a health procedure. + An identifier that denotes a health procedure. + health procedure identifier + + + + + + + + + A temporal information that is a component of a health activity beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of the health activity. + A temporal information that is a component of a health activity beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of the health activity. + health activity beginning temporal information + + + + + + + + + A temporal information that is a component of a health procedure beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of the health procedure. + A temporal information that is a component of a health procedure beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of the health procedure. + health procedure beginning temporal information + + + + + + + + + A temporal information that is a component of a health activity ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of the health activity. + A temporal information that is a component of a health activity ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of the health activity. + health activity ending temporal information + + + + + + + + + A temporal information that is a component of a health procedure ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of the health procedure. + A temporal information that is a component of a health procedure ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of the health procedure. + health procedure ending temporal information + + + + + + + + + + + + + + + + + + + + + A pragmatically accepted statement that states the presence of a pathological condition for an organism. + A pragmatically accepted statement that states the presence of a pathological condition for an organism. + pathological condition presence statement + + + + + + + + + + + + + + + A temporally qualifying statement that qualifies the clinically identified appearance of a disorder or a disease, or the beginning of a pathological process. + A temporally qualifying statement that qualifies the clinically identified appearance of a disorder or a disease, or the beginning of a pathological process. + pathological condition start temporally qualifying statement + + + + + + + + + + + + + + + A temporally qualifying statement that qualifies the clinically identified disappearance of a disorder or a disease, or the ending of a pathological process. + A temporally qualifying statement that qualifies the clinically identified disappearance of a disorder or a disease, or the ending of a pathological process. + pathological condition end temporally qualifying statement + + + + + + + + + A temporal information that is a component of a pathological condition start temporallly qualifying statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the clinically identified start of the pathological condition. + A temporal information that is a component of a pathological condition start temporallly qualifying statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the clinically identified start of the pathological condition. + pathological condition start temporal information + + + + + + + + + A temporal information that is a component of a pathological condition end temporallly qualifying statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the clinically identified end of the pathological condition. + A temporal information that is a component of a pathological condition end temporallly qualifying statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the clinically identified end of the pathological condition. + pathological condition end temporal information + + + + + + + + + + + + + + + A service agreement specification identifying an organism for whom a healthcare service delivery aims at providing a desired effect to its health status. + + healthcare service organism specification + + + + + + + + + A facility that bears a healthcare function - WiP. + healthcare facility + + + + + + + + + A role that inheres in an organisation and is realized by providing some healthcare service delivery. + healthcare organization role + + + + + + + + + + + + + + + An organisation that bears a healthcare organisation role. + healthcare organization + + + + + + + + + + + + + + + + + + + A health provider who is a member of a healthcare organisation. + + healthcare provider + + + + + + + + + + + + + + + A health procedure that is part of a healthcare service delivery and that is performed by a healthcare worker while realizing its health care worker role. + healthcare procedure + + + + + + + + + + + + + + + A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization. + + + healthcare organization service delivery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes. + + + healthcare organization clinical visit + + + + + + + + + A service delivery that aims to support health services without directly providing a desired effect on the health status of individuals or communities. + + ancillary care service delivery + + + + + + + + + A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities. + + custodial care service delivery + + + + + + + + + A healthcare service that aims at providing a desired effect on the health status of a community. + + populational healthcare service + + + + + + + + + A temporally-connected healthcare organization clinical visit that aims to improve, maintain or restore the health of some participating organism. + + healthcare organization clinical encounter + + + + + + + + + + + + + + + + + + + A healthcare encounter during which the recipient is located in a healthcare facility at some time. + + facility-supported healthcare encounter + + + + + + + + + + + + + + + + An identifier that denotes a public provincial health insurance record. + + public provincial health identifier + + + + + + + + + An identifier that denotes a building administered by a healthcare organization for the purpose of providing healthcare to a patient or patient population. + healthcare facility identifier + + + + + + + + + + + + 1 + + + + An identifier that denotes a healthcare organization. + healthcare organization identifier + + + + + + + + + + + + + + + A healthcare organisation clinical visit where the patient physically attends to a healthcare facility, but where there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient. + + outpatient visit + + + + + + + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient. + + inpatient visit + + + + + + + + + An inpatient visit that does not extend overnight. + + day inpatient visit + + + + + + + + + + + + + + + A day inpatient visit which includes a surgical procedure. + + day inpatient surgery visit + + + + + + + + + An inpatient visit located in a hospital facility requested by a physician, that may extends overnight. + + + hospitalization + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. +It is not necessarily an immediate inpatient subsequent visit. + + + emergency department visit + + + + + + + + + + + + + + + + An emergency department visit and an inpatient visit, where there is usually limited accommodation and where the goal is to stabilise a life-threatening condition or decide whether the clinical situation requires a hospitalisation visit. + + emergency department inpatient visit + + + + + + + + + + + + + + + + + An emergency department visit and an outpatient visit. + There is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient + + emergency department outpatient visit + + + + + + + + + An outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions. + + walk-in clinic visit + + + + + + + + + + + + + + + An outpatient visit which includes a surgical procedure. + + outpatient surgery visit + + + + + + + + + + + + + + + An outpatient visit which includes a diagnostic procedure. + + outpatient diagnostic visit + + + + + + + + + + + + + + + + An immediate subsequent visit healthcare organisation visit for a given patient that was participating in another healthcare organisation visit for the same organisation just prior to this visit. + + immediate inpatient subsequent visit + + + + + + + + + + + + + + + + + + + + + + + + + An information content entity describing the type of visit that occured prior to an immediate inpatient subsequent visit. + + prior visit category to an inpatient visit + + + + + + + + + A healthcare organisation service delivery where the main entity of interest is a still born. + + still born healthcare service + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + A healthcare organization clinical visit during which a birth statement was produced regarding the birth of the main patient visit beneficiary. + In the case of human health the specified organism refers to the child born during the visit. + + healthcare birth visit + + + + + + + + + Patient hospitalized directly from home. + Patient transferred from a healthcare organization emergency department to be hospitalized by a different healthcare organization. + an inpatient visit that is not immedately following another healthcare organisation clinical visit in the same organisation, and is not a healthcare birth visit + + inpatient visit from an external location + + + + + + + + + + + + + + + + + + + An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + Considérer axomatisation séquentielle + + + ambulance initiated emergency department visit + + + + + + + + + A healthcare organization service delivery where the main entity of interest is a human cadaver that was not delivered just prior to this service. + + cadaver service + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + A healthcare organization clinical visit during which a death statement was produced regarding the death of the main patient visit beneficiary. + A healthcare organization clinical visit during which the patient died. + + healthcare visit of expiration + + + + + + + + + + + + + + + A directive information entity that aims at directing what health procedures or healthcare organization services are recommended after this visit. + + visit discharge specification + + + + + + + + + + + + + + + A visit discharge specification that aims at directing to which healthcare organisation the patient should be transferred after the end of the current visit. + + visit transfer specification + + + + + + + + + + + + + + + An information content entity that is part of a visit transfer specification and is about the type of healthcare organization specified. + + visit transfer specification category + + + + + + + + + + + + + + + + + + + + + + + A visit discharge specification for a given clinical visit that has no visit transfer specification. + + visit discharge specification for home + + + + + + + + + + + + + + + + + + + + + + + A healthcare organization clinical visit ended at the initiative of the patient without physician approval. + + visit ended by the patient + + + + + + + + + A visit ended by the patient without notifying the healthcare organization. + + visit ended by the patient without notification + + + + + + + + + An emergency department visit with a triage encounter but no further encounter. + + triage-only emergency department visit + + + + + + + + + + An emergency department visit and a visit ended by the patient and some treatment healthcare procedure was provided. + + emergency department visit with partial treatment + + + + + + + + + An identifier that denotes a diagnosis related group. + DRG code + + visit diagnosis related group code + + + + + + + + + + + + + + + + + + + + + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + + + healthcare organization service delivery beginning statement + + + + + + + + + + + + + + + + + + + + + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + + + healthcare organization service delivery ending statement + + + + + + + + + + + + 1 + + + + An information content entity that contains the information required to manage the insurance coverage of an insured individual. + + public provincial health insurance record + + + + + + + + + A role that is borne by an human that is the primary beneficiary of a health insurance plan and so is responsible for its associated contract. + primary health insurance beneficiary human role + + + + + + + + + + + + + + + + + + + + A human that has a role of primary health insurance benificiary role + primary health insurance beneficiary human + + + + + + + + + + + + + + + + + + 1 + + + + A statement that indicates the postal address of the primary residence for a primary health insurance beneficiary of a public health provincial plan. + public provincial health insurance primary residence statement + + + + + + + + + + + + + + + provincial health insurance primary residence statement beginning + + + + + + + + + + + + + + + + + + + A healthcare organization clinical visit for a given patient that was participating in another healthcare organisation clinical visit just prior to this visit. + + immediate subsequent visit + + + + + + + + + An immediate subsequent visit where both visits are under the responsability of the same healthcare organisation. + + immediate subsequent visit in same organization + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + direct ambulance initiated hospitalization + + + + + + + + + A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider. + + ambulance paramedics visit + + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit. + + ED by ambulance initiated hospitalization + + + + + + + + + A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit. + ICU admission specification + + + + + + + + + A service agreement specification for a clinical visit admission. + clinical visit agreement specification + + + + + + + + + A clinical visit agreement specification mandating the urgency level of the clinical visit. + clinical visit urgency level specification + + + + + + + + + A clinical visit urgency level specification mandating the urgency level of the hospitalization admission. + hospitalization admission urgency level specification + + + + + + + + + A clinical visit agreement specification mandating the type of unit required for a clinical visit. + clinical visit unit type specification + + + + + + + + + + + + + + + A clinical visit agreement specification mandating the admitting physician. + hospitalization admitting physician specification + + + + + + + + + + + + + + + A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members + It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department. + It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon). + healthcare physician service + + + + + + + + + + + + + + + + + + + + + A primary residence statement that states the type of living environment of a patient immediately prior to a clinical visit. + living environment type prior to clinical visit statement + + + + + + + + + + + + + + + An eukaryote that is the bearer of a patient role. + patient + + + + + + + + + + + + + + + A role born by an organism which is the primary recipient in a healthcare organization clinical visit. + patient role + + + + + + + + + + + + + + + + A patient that is a Homo sapiens. + human patient + + + + + + + + + + + + 1 + + + + A healthcare organization identifier that denotes a physician service. + healthcare physician service identifier + + + + + + + + + + + + + + + An identifier that denotes a healthcare organization service delivery. + An identifier that denotes a healthcare organization service delivery. + + healthcare organization service delivery identifier + + + + + + + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + healthcare organization service delivery beginning temporal information + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + healthcare organization service delivery ending temporal information + + + + + + + + + A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. + A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. + canadian healthcare facility postal code + + + + + + + + + A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + canadian healthcare organization postal code + + + + + + + + + A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. + A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. + canadian healthcare facility forward sorting area code + + + + + + + + + A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + canadian healthcare organization forward sorting area code + + + + + + + + + + + + + + + + + + + + + + + + + + + A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. + A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. + health organization clinical visit pathological condition impact statement + + + + + + + + + A healthcare procedure where the responsible healthcare worker comes to the conclusion that a clinical visit can end. + clinical visit ending determination + + + + + + + + + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + pathological condition impact type on clinical visit + + + + + + + + + + + + + + + + + + + + human clinical visit specified patient + + + + + + + + + + + + + + 1 + + + + + + An identifier that denotes a healthcare provider. + + + healthcare provider identifier + + + + + + + + + + + + + + + + + + + + facility-supported clinical visit + + + + + + + + + + + + + + + A postal address that enables an agent to locate a facility. + facility address + + + + + + + + + + + + + + + + canadian facility address + + + + + + + + + + + + + + + An information content entity that aims at representing the various forms of care provided within the healthcare organization clinical visit as approximated by a case-mix group definition. + DRG + + diagnosis related group + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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, and that may be concretized as a realizable entity that, if realized, 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. + 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + Clint Dowland + 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 + https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 + + + + + + + + + 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 + + + + + + + + + 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 + text + textual entity + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 code set of PubMed identifiers associated with journal articles. + + A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. + Justin Whorton + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID registry + Original proposal from Bjoern, discussions at IAO calls + https://github.com/information-artifact-ontology/IAO/issues/237 + centrally registered identifier registry + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + identifier + 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. + Justin Whorton + Mathias Brochhausen + proper name + https://github.com/information-artifact-ontology/IAO/issues/237 + Mathias Brochhausen + Sep 29, 2016: The current definition has been amended from the previous version: "A proper name 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." to more accuratly reflect the necessary and sufficient condition on the class. (MB) + identifier + + + + + + + + + + + + + + + + + + + + A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. + Justin Whorton + Mathias Brochhausen + dubbing process + naming + https://github.com/information-artifact-ontology/IAO/issues/237 + Mathias Brochhausen + identifier creating process + + + + + + + + + + + + + + + An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. + Alan Ruttenberg + Justin Whorton + Mathias Brochhausen + code map + code system + codeset + coding system + controlled vocabulary + https://github.com/information-artifact-ontology/IAO/issues/237 + Alan Ruttenberg + Clint Dowland + Matt Diller + Sarah Bost + William R. Hogan + Code sets might include non-entities/things (e.g. missing thumbs). + Does not imply absence vs. presence of any taxonomy. + Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. + Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. + +When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). + For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). + For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. + Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. + The information content entities do not denote each other. + code set + + + + + + + + + + + + + + + + + + + + + Connor, John, born on 28/2/1985 + +Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + + human birth statement + + + + + + + + + + + + + + + + A state sanctioned human birth statement. + A state sanctioned human birth statement. + + civil birth record + + + + + + + + + + + + + + + + + + + + + Reese, Kyle died in 1984 + A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. + A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. + + human death statement + + + + + + + + + + + + + + + + A state sanctioned human death statement. + A state sanctioned human death statement. + + civil death record + + + + + + + + + + + + + + + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + human birth temporal information + + + + + + + + + + + + + + + A temporal information that is a component of a human death statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the death of this human. + A temporal information that is a component of a human death statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the death of this human. + human death temporal information + + + + + + + + + An information content entity that denotes the biological sex of an organism. + An information content entity that denotes the biological sex of an organism. + biological sex information content entity + + + + + + + + + A biological sex information content entity that denotes the biological sex of a human. + A biological sex information content entity that denotes the biological sex of a human. + + human biological sex information content entity + + + + + + + + + + + + + + + + + An information content entity that denotes a biological sex or a gender identity of a human. + An information content entity that denotes a biological sex or a gender identity of a human. + + human biological sex or gender identity information content entity + + + + + + + + + + + + + + 1 + + + + + + 'Goose' (the name of a cat) + An identifier that denotes a particular organism. + An identifier that denotes a particular organism. + + organism identifier + + + + + + + + + + + + + + 1 + + + + + + An organism identifier that denotes a particular human. + An organism identifier that denotes a particular human. + + + human identifier + + + + + + + + + + + + + + + + + + + + + A pragmatically accepted statement stating the biological sex of a human. + A pragmatically accepted statement stating the biological sex of a human. + + human biological sex statement + + + + + + + + + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + human birth date + + + + + + + + + A human death temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + A human death temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + human death date + + + + + + + + + A pragmatically accepted statement that states characteristics of the primary residence of an individual at a given moment in time. + primary residence statement + + + + + + + + + An information content entity that aims at representing a type of living environment applicable to a primary residence. + living environment type + + + + + + + + + + + + 1 + + + + + Human birth date with data property + MPHPO human birth date + + + + + + + + + + + + 1 + + + + + human biological sex ICE with data property + MPHPO human biological sex information content entity + + + + + + + + + + + + 1 + + + + + ICU admission specification with data property + MPHPO ICU admission specification + + + + + + + + + + + + 1 + + + + + hospitalization admission urgency level specification with data property + MPHPO hospitalization admission urgency level specification + + + + + + + + + + + + 1 + + + + + healthcare physician service identifier with data property + MPHPO healthcare physician service identifier + + + + + + + + + + + + 1 + + + + + pathological condition impact type on clinical visit with data property + MPHPO pathological condition impact type on clinical visit + + + + + + + + + + + + 1 + + + + + pathological condition sub-group name with data property + MPHPO pathological condition sub-group name + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery beginning temporal information with data property + MPHPO healthcare organization service delivery beginning temporal information + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery ending temporal information with data property + MPHPO healthcare organization service delivery ending temporal information + + + + + + + + + + + + 1 + + + + + living environment type with data property + MPHPO living environment type + + + + + + + + + Viruses + + Viruses + + + + + + + + + Bacteria + eubacteria + + Bacteria + + + + + + + + + Archaea + + Archaea + + + + + + + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota + + + + + + + + + Homo sapiens + human + human being + + + + Homo sapiens + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + + planned process + + + + + + + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization + + + + + + + + + plan + The plan of researcher X to perform an experiment according to a protocol. + + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. + AR, BP, JM, MC, PRS + branch derived + plan + + + + + + + + + + + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant. + note: defined class + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06 + symptom + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:21:20Z + disease + + + + + + + + + A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:39:44Z + disorder + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:53:49Z + bodily process + + + + + + + + + A bodily process that is clinically abnormal. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:54:29Z + pathological bodily process + + + + + + + + + A pattern of signs and symptoms that typically co-occur. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=32 + creation date: 2009-11-24T04:51:11Z + syndrome + + + + + + + + + A disorder that involves some structural damage that is immediately caused by a catastrophic external force. + At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. + Albert Goldfain +Sagar Jain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 + +OGMS call adoption- 16 SEPT 2015 +https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit + creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015 + injury + + + + + + + + + An abnormal material entity that is part of a patient and hypothesized to be clinically relevant. + Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension + physical sign + + + + + + + + + An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant. + processual sign + + + + + + + + + An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant. + Example: the color of a rash; the shape of a melanoma + qualitative sign + + + + + + + + + A material entity that is a human made strcuture with firm connection between its foundation and the ground. + Mathias Brochhausen + http://de.wikipedia.org/wiki/Bauwerk + "Building" is a subclass of this. + This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". + architectural structure + + + + + + + + + + + + + + + + + + + + + + + + + + + An architectural structure that bears some function. + Mathias Brochhausen + facility + + + + + + + + + + 09/09/2017 + + + + + + + + + An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way. + social identity information content entity + + + + + + + + + A social identity information content entity that is about whether some person identifies as some gender. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + gender identity information content entity + + + + + + + + + A gender identity information content entity that is about some person's identifying as female in gender. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + female gender identity information content entity + + + + + + + + + A gender identity information content entity that is about some person's identifying as male in gender. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + male gender identity information content entity + + + + + + + + + A gender identity information content entity that is about some person's identifying as non-binary in gender. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + non-binary identity information content entity + + + + + + + + + A generically dependent continuant that is a building block of information or a combination thereof. + Contrarily to ICE, informational entities are not necessarily about some things. Therefore they includes ICE, but also words like 'unicorn', letters like 'a' or pictures of unicorns. + informational entity + + + + + + + + + + + + + + + + + + + + + + + + + A statement for which there is at least one contributor such that if it/he acts upon it, it/he will treat it as true. + A statement for which there is at least one contributor such that if it/he acts upon it, it/he will treat it as true. + pragmatically accepted statement + + + + + A statement for which there is at least one contributor such that if it/he acts upon it, it/he will treat it as true. + Note that the contributor does not need to believe in the truth of the statement to be disposed to act as if it was true. + + + + + + + + + + + + + + + + + + + + + + + + + A date of birth recorded in the French civil registrar. + A pragmatically accepted statement authored by a governement or a related organization such that if this organization acts upon it, it will treat it as true. + A pragmatically accepted statement authored by a governement or a related organization such that if this organization acts upon it, it will treat it as true. + government sanctioned statement + + + + + + + + + + An informational entity that can be filled by an informational filler. + An informational entity that can be filled by an informational filler. + informational slot + + + + + + + + + + + + + + + + + + + An informational entity that fills an informational slot. + An informational entity that fills an informational slot. + informational filler + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + + + 1 + + + + + + + 1 + + + + A postal address that can be used to help the delivery of something in Canada. + A postal address that can be used to help the delivery of something in Canada. + canadian postal address + + + + + + + + + + + + + + + An identifier that denotes a Canadian municipality (as determined by provincial/territorial legislation) or a Canadian area treated as a municipal equivalent for statistical purposes (e.g., Indian reserves, Indian settlements and unorganized territories). + An identifier that denotes a Canadian municipality (as determined by provincial/territorial legislation) or a Canadian area treated as a municipal equivalent for statistical purposes (e.g., Indian reserves, Indian settlements and unorganized territories). + canadian census subdivision identifier + + + + + + + + + An identifier that denotes a Canadian province or a Canadian territory. + An identifier that denotes a Canadian province or a Canadian territory. + canadian first-order administrative region identifier + + + + + + + + + An identifier that denotes a geographical region on which is based the first three characters of a Canadian postal code. + An identifier that denotes a geographical region on which is based the first three characters of a Canadian postal code. + canadian forward sorting area code + + + + + + + + + + + + + + + An identifier that denotes a city and is intended to be used as part of a postal address. + An identifier that denotes a city and is intended to be used as part of a postal address. + postal address city + + + + + + + + + + + + + + + An identifier that denotes a country and is intended to be used as part of a postal address. + An identifier that denotes a country and is intended to be used as part of a postal address. + postal address country + + + + + + + + + + + + 1 + + + + A postal code that denotes some geographical region in Canada. + A postal code that denotes some geographical region in Canada. + canadian postal code + + + + + + + + + + + + + + + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + It is an open question whether the mereological sum of a request with any other ICE is also a request + request + + + + + It is an open question whether the mereological sum of a request with any other ICE is also a request + hence the definitional necessary condition. + + + + + + + + + + + + + + + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + An information content entity that is the output of a service agreement negociation. + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + service agreement specification + + + + + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + service offer + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + It is an open question whether offering to cook for one's spouse is a service offer. + A service is usually offered for a compensation + + + + + + + + + + + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + temporally qualifying statement + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + More formally, this amount to states that a temporal region overlaps (in the sense of Allen's temporal relations) with a temporal region during which some entity exists. + + + + + + + + + + + + + + + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + process temporally qualifying statement + + + + + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process temporally qualifying statement qualifying temporally the beginning of a process. + process beginning statement + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process that is a mereological sum of temporally disconnected processes has only one process beginning. + + + + + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process temporally qualifying statement qualifying temporally the ending of a process. + process ending statement + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process that is a mereological sum of temporally disconnected processes has only one process ending. + + + + + + + + + + + + + + + + + + + + + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + service agreement negotiation + + + + + + + + + + + + + + + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + service delivery + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + All service deliveries are directed by a service agreement specification, even if this specification is concretized only mentally. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A plan of an agent to act as if some statement was true. + A plan of an agent to act as if some statement was true. + agent plan to act as if some statement was true + + + + + + + + + + + + + + + A continuant appearance statement that temporally qualifies the apparition of a plan to act as if some statement was true. + A continuant appearance statement that temporally qualifies the apparition of a plan to act as if some statement was true. + temporal qualification of the appearance of a plan to act as if some statement was true + + + + + + + + + + + + + + + A continuant disappearance statement that temporally qualifies the disappearance of a plan to act as if some statement was true. + A continuant disappearance statement that temporally qualifies the disappearance of a plan to act as if some statement was true. + temporal qualification of the disappearance of a plan to act as if some statement was true + + + + + + + + + + + + + + + 'May 5th 2023' for characterizing temporally a plan that existed from 8 AM to noon on this day. + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some continuant exists. + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some continuant exists. + continuant temporally qualifying statement + + + + + + + + + A continuant temporally qualifying statement qualifying temporally the appearance of a continuant. + A continuant temporally qualifying statement qualifying temporally the appearance of a continuant. + continuant appearance statement + + + + + + + + + A continuant temporally qualifying statement temporally qualifying the disappearance of a continuant. + A continuant temporally qualifying statement temporally qualifying the disappearance of a continuant. + continuant disappearance statement + + + + + + + + + + + + 1 + + + 4 Km + An information content entity whose structure and content follow a template. + specified value + + + + + + + + + numerical specified value + + + + + + + + + + + + 1 + + + + + + + 1 + + + + unit qualified scalar specified value + + + + + + + + + + + + + + + unit + + + + + + + + + + + + + + + + + + An entity that is a disorder, a disease or a pathological bodily process + An entity that is a disorder, a disease or a pathological bodily process + pathological condition + + + + + + + + + + + + + + 1 + + + + + + An information content entity that denotes a one-dimension temporal region. + An information content entity that denotes a one-dimension temporal region. + + temporal information + + + + + + + + + The following is derived from https://en.wikipedia.org/wiki/Statement_(logic): + +Examples of sentences that are (or make) statements: +"Socrates is a man." +"A triangle has three sides." +"Madrid is the capital of Spain." +"There are five ducks on the lake" +"The BRAF V600E mutation causes breast cancer" + +Examples of sentences that are not (or do not make) statements: +"Who are you?" +"Run!" +"Greenness perambulates." +"I had one grunch but the eggplant over there." +"The King of France is wise." +"Broccoli tastes good." + +The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste. + An information content entity expressing a declarative sentence that is either true or false. + From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21): +"A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities." +---- +Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO? + Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made. + +The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth. + statement + + + + + + + + + + + + + + + + + + + + + A measurement datum that quantifies the level of confidence an agent has that a particular piece of information is true. + confidence level + + + + + + + + + + + + + + + + + + + + A Material Entity that is capable of performing Planned Acts + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + Agent + + + + + + + + + A Realizable Entity that inheres in an Agent to the extent of that Agent's capacity to realize it in Intentional Acts of a certain type. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + Agent Capability + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/RIDDLE.owl b/RIDDLE.owl index d99e26a..2412405 100644 --- a/RIDDLE.owl +++ b/RIDDLE.owl @@ -7,24 +7,22 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:HOSO="http://purl.obolibrary.org/obo/HOSO.owl#" - xmlns:IOIO="http://purl.obolibrary.org/obo/IOIO#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:HEPRO="http://purl.obolibrary.org/obo/HEPRO#" - xmlns:HOSO1="http://purl.obolibrary.org/obo/HOSO#" + xmlns:MPHPO="http://purl.obolibrary.org/obo/MPHPO#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:OpenLHS-Core="http://purl.obolibrary.org/obo/OpenLHS-Core#" xmlns:CommonCoreOntologies="http://www.ontologyrepository.com/CommonCoreOntologies/"> - - None + + Ontology for project RIDDLE - RIDDLE project ontology - 2023-10-12 + Mortality Prediction for Hospitalized Patient Ontology + 2024-08-02 @@ -301,38 +299,21 @@ - + - - HEPRO-H + + Subset for RIDDLE project + MPHPO-Slim - + - - HOSO classes relevant to humans. - HOSO-H - - - - - - - - - - - - - - - - - IOIO classes relevent to humans. - IOIO-H + + OpenLHS classes relevant to humans. + OpenLHS-H @@ -460,6 +441,25 @@ + + + + + + + + + ISO8601 DateTime + + + + + + + + + + + + + has textual representation + + + + + + + + + has value + + + + + + + + + has numerical value + + + + + + + + + has temporal value + + + + + + + + + has text value + + + + - + @@ -3280,7 +3331,8 @@ every c that is a concretization of g specifically denotes r An individual identifier that denotes a health provider. - + + health provider identifier @@ -3290,8 +3342,15 @@ every c that is a concretization of g specifically denotes r + + + + 1 + + + A health provider identifier that is used to denote a person authorised to act as a physician. - + physician identifier @@ -3310,7 +3369,7 @@ every c that is a concretization of g specifically denotes r A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities. This usually includes health professional like physicians, nurses or pharmacists etc. It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants. - + health provider role @@ -3319,7 +3378,7 @@ It could also includes non professionals like patient attendant but it would exc - + @@ -3327,7 +3386,8 @@ It could also includes non professionals like patient attendant but it would exc An organism that is the bearer of a health provider role. - + + health provider @@ -3337,8 +3397,8 @@ It could also includes non professionals like patient attendant but it would exc - TBD - + A health procedure that include a diagnostic procedure - TBD. + diagnostic health procedure @@ -3348,8 +3408,8 @@ It could also includes non professionals like patient attendant but it would exc - TBD - + A health procedure that includes a surgical procedure - TBD. + surgical health procedure @@ -3524,6 +3584,7 @@ It could also includes non professionals like patient attendant but it would exc A directive information entity that aims to direct a health procedure. A directive information entity that aims to direct a health procedure. + health procedure specification @@ -3685,6 +3746,7 @@ It could also includes non professionals like patient attendant but it would exc A service agreement specification identifying an organism for whom a healthcare service delivery aims at providing a desired effect to its health status. + healthcare service organism specification @@ -3694,7 +3756,7 @@ It could also includes non professionals like patient attendant but it would exc - TBD + A facility that bears a healthcare function - WiP. healthcare facility @@ -3740,14 +3802,8 @@ It could also includes non professionals like patient attendant but it would exc - - - - - - - A health provider who is a member of a healthcare organisation. + healthcare provider @@ -3780,7 +3836,8 @@ It could also includes non professionals like patient attendant but it would exc A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization. - + + healthcare organization service delivery @@ -3799,7 +3856,13 @@ It could also includes non professionals like patient attendant but it would exc - + + + + + + + @@ -3810,7 +3873,8 @@ It could also includes non professionals like patient attendant but it would exc A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes. - + + healthcare organization clinical visit @@ -3821,7 +3885,7 @@ It could also includes non professionals like patient attendant but it would exc A service delivery that aims to support health services without directly providing a desired effect on the health status of individuals or communities. - + ancillary care service delivery @@ -3832,7 +3896,7 @@ It could also includes non professionals like patient attendant but it would exc A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities. - + custodial care service delivery @@ -3843,7 +3907,7 @@ It could also includes non professionals like patient attendant but it would exc A healthcare service that aims at providing a desired effect on the health status of a community. - + populational healthcare service @@ -3854,7 +3918,7 @@ It could also includes non professionals like patient attendant but it would exc A temporally-connected healthcare organization clinical visit that aims to improve, maintain or restore the health of some participating organism. - + healthcare organization clinical encounter @@ -3874,10 +3938,8 @@ It could also includes non professionals like patient attendant but it would exc - - A healthcare encounter during which the recipient is located in a healthcare facility at some time. - + facility-supported healthcare encounter @@ -3887,6 +3949,7 @@ It could also includes non professionals like patient attendant but it would exc + @@ -3894,7 +3957,7 @@ It could also includes non professionals like patient attendant but it would exc An identifier that denotes a public provincial health insurance record. - + public provincial health identifier @@ -3930,9 +3993,15 @@ It could also includes non professionals like patient attendant but it would exc - + + + + + + + A healthcare organisation clinical visit where the patient physically attends to a healthcare facility, but where there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient. - + outpatient visit @@ -3941,15 +4010,21 @@ It could also includes non professionals like patient attendant but it would exc - + + + + + + + A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient. - + inpatient visit @@ -3960,7 +4035,7 @@ It could also includes non professionals like patient attendant but it would exc An inpatient visit that does not extend overnight. - + day inpatient visit @@ -3977,7 +4052,7 @@ It could also includes non professionals like patient attendant but it would exc A day inpatient visit which includes a surgical procedure. - + day inpatient surgery visit @@ -3988,7 +4063,8 @@ It could also includes non professionals like patient attendant but it would exc An inpatient visit located in a hospital facility requested by a physician, that may extends overnight. - + + hospitalization @@ -3997,10 +4073,17 @@ It could also includes non professionals like patient attendant but it would exc - + + + + + + + A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. It is not necessarily an immediate inpatient subsequent visit. - + + emergency department visit @@ -4017,10 +4100,8 @@ It is not necessarily an immediate inpatient subsequent visit. - - An emergency department visit and an inpatient visit, where there is usually limited accommodation and where the goal is to stabilise a life-threatening condition or decide whether the clinical situation requires a hospitalisation visit. - + emergency department inpatient visit @@ -4037,11 +4118,10 @@ It is not necessarily an immediate inpatient subsequent visit. - - + An emergency department visit and an outpatient visit. - there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient - + There is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient + emergency department outpatient visit @@ -4051,8 +4131,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions - + An outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions. + walk-in clinic visit @@ -4068,8 +4148,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit which includes a surgical procedure - + An outpatient visit which includes a surgical procedure. + outpatient surgery visit @@ -4085,8 +4165,8 @@ It is not necessarily an immediate inpatient subsequent visit. - an outpatient visit which includes a diagnostic procedure - + An outpatient visit which includes a diagnostic procedure. + outpatient diagnostic visit @@ -4103,10 +4183,8 @@ It is not necessarily an immediate inpatient subsequent visit. - - An immediate subsequent visit healthcare organisation visit for a given patient that was participating in another healthcare organisation visit for the same organisation just prior to this visit. - + immediate inpatient subsequent visit @@ -4133,7 +4211,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity describing the type of visit that occured prior to an immediate inpatient subsequent visit. - + prior visit category to an inpatient visit @@ -4144,7 +4222,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organisation service delivery where the main entity of interest is a still born. - + still born healthcare service @@ -4175,27 +4253,9 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - - - - - 1 - - - - - - - A healthcare organization clinical visit during which a birth statement was produced regarding the birth of the main patient visit beneficiary. In the case of human health the specified organism refers to the child born during the visit. - + healthcare birth visit @@ -4208,7 +4268,7 @@ It is not necessarily an immediate inpatient subsequent visit. Patient hospitalized directly from home. Patient transferred from a healthcare organization emergency department to be hospitalized by a different healthcare organization. an inpatient visit that is not immedately following another healthcare organisation clinical visit in the same organisation, and is not a healthcare birth visit - + inpatient visit from an external location @@ -4217,10 +4277,21 @@ It is not necessarily an immediate inpatient subsequent visit. - - + + + + + + + + + + + An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. - + Considérer axomatisation séquentielle + + ambulance initiated emergency department visit @@ -4231,7 +4302,7 @@ It is not necessarily an immediate inpatient subsequent visit. A healthcare organization service delivery where the main entity of interest is a human cadaver that was not delivered just prior to this service. - + cadaver service @@ -4262,27 +4333,9 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - - - - - 1 - - - - - - - A healthcare organization clinical visit during which a death statement was produced regarding the death of the main patient visit beneficiary. A healthcare organization clinical visit during which the patient died. - + healthcare visit of expiration @@ -4299,7 +4352,7 @@ It is not necessarily an immediate inpatient subsequent visit. A directive information entity that aims at directing what health procedures or healthcare organization services are recommended after this visit. - + visit discharge specification @@ -4316,7 +4369,7 @@ It is not necessarily an immediate inpatient subsequent visit. A visit discharge specification that aims at directing to which healthcare organisation the patient should be transferred after the end of the current visit. - + visit transfer specification @@ -4333,7 +4386,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that is part of a visit transfer specification and is about the type of healthcare organization specified. - + visit transfer specification category @@ -4357,9 +4410,8 @@ It is not necessarily an immediate inpatient subsequent visit. - A visit discharge specification for a given clinical visit that has no visit transfer specification. - + visit discharge specification for home @@ -4383,9 +4435,8 @@ It is not necessarily an immediate inpatient subsequent visit. - A healthcare organization clinical visit ended at the initiative of the patient without physician approval. - + visit ended by the patient @@ -4396,7 +4447,7 @@ It is not necessarily an immediate inpatient subsequent visit. A visit ended by the patient without notifying the healthcare organization. - + visit ended by the patient without notification @@ -4407,7 +4458,7 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit with a triage encounter but no further encounter. - + triage-only emergency department visit @@ -4419,7 +4470,7 @@ It is not necessarily an immediate inpatient subsequent visit. An emergency department visit and a visit ended by the patient and some treatment healthcare procedure was provided. - + emergency department visit with partial treatment @@ -4431,7 +4482,7 @@ It is not necessarily an immediate inpatient subsequent visit. An identifier that denotes a diagnosis related group. DRG code - + visit diagnosis related group code @@ -4455,7 +4506,8 @@ It is not necessarily an immediate inpatient subsequent visit. A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. - + + healthcare organization service delivery beginning statement @@ -4479,7 +4531,8 @@ It is not necessarily an immediate inpatient subsequent visit. A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. - + + healthcare organization service delivery ending statement @@ -4497,7 +4550,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that contains the information required to manage the insurance coverage of an insured individual. - + public provincial health insurance record @@ -4528,12 +4581,6 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - A human that has a role of primary health insurance benificiary role primary health insurance beneficiary human @@ -4592,15 +4639,8 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - A healthcare organization clinical visit for a given patient that was participating in another healthcare organisation clinical visit just prior to this visit. - + immediate subsequent visit @@ -4611,117 +4651,361 @@ It is not necessarily an immediate inpatient subsequent visit. An immediate subsequent visit where both visits are under the responsability of the same healthcare organisation. - + immediate subsequent visit in same organization - + - - - An identifier that denotes a healthcare organization service delivery. - An identifier that denotes a healthcare organization service delivery. - healthcare organization service delivery identifier + + + + + + + + + + + + + An hospitalization for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + direct ambulance initiated hospitalization - + - - - A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. - A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. - healthcare organization service delivery beginning temporal information + + + A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider. + + ambulance paramedics visit - + - - - A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. - A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. - healthcare organization service delivery ending temporal information + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit. + + ED by ambulance initiated hospitalization - + - - - A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. - A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. - canadian healthcare facility postal code + + + A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit. + ICU admission specification - + - - - A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. - A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. - canadian healthcare organization postal code + + + A service agreement specification for a clinical visit admission. + clinical visit agreement specification - + - - - A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. - A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. - canadian healthcare facility forward sorting area code + + + A clinical visit agreement specification mandating the urgency level of the clinical visit. + clinical visit urgency level specification - + - - - A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. - A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. - canadian healthcare organization forward sorting area code + + + A clinical visit urgency level specification mandating the urgency level of the hospitalization admission. + hospitalization admission urgency level specification - + - - + + + A clinical visit agreement specification mandating the type of unit required for a clinical visit. + clinical visit unit type specification + + + + + + + + - - + + + A clinical visit agreement specification mandating the admitting physician. + hospitalization admitting physician specification + + + + + + + + - - + + - A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. - A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. - health organization clinical visit pathological condition impact statement + A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members + It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department. + It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon). + healthcare physician service - + - - - A healthcare procedure where the responsible healthcare worker comes to the conclusion that a clinical visit can end. + + + + + + + + + + + + + + + A primary residence statement that states the type of living environment of a patient immediately prior to a clinical visit. + living environment type prior to clinical visit statement + + + + + + + + + + + + + + + An eukaryote that is the bearer of a patient role. + patient + + + + + + + + + + + + + + + A role born by an organism which is the primary recipient in a healthcare organization clinical visit. + patient role + + + + + + + + + + + + + + + + A patient that is a Homo sapiens. + human patient + + + + + + + + + + + + 1 + + + + A healthcare organization identifier that denotes a physician service. + healthcare physician service identifier + + + + + + + + + + + + + + + An identifier that denotes a healthcare organization service delivery. + An identifier that denotes a healthcare organization service delivery. + + healthcare organization service delivery identifier + + + + + + + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + healthcare organization service delivery beginning temporal information + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + healthcare organization service delivery ending temporal information + + + + + + + + + A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. + A canadian postal code that denotes a geographical region where a canadian healthcare facility is located. + canadian healthcare facility postal code + + + + + + + + + A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + A canadian postal code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + canadian healthcare organization postal code + + + + + + + + + A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. + A canadian forward sorting area code that denotes a geographical region where a canadian healthcare facility is located. + canadian healthcare facility forward sorting area code + + + + + + + + + A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + A canadian forward sorting area code that denotes a geographical region where postal payloads are to be delivered for a canadian healthcare organization. + canadian healthcare organization forward sorting area code + + + + + + + + + + + + + + + + + + + + + + + + + + + A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. + A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit. + health organization clinical visit pathological condition impact statement + + + + + + + + + A healthcare procedure where the responsible healthcare worker comes to the conclusion that a clinical visit can end. clinical visit ending determination @@ -4752,13 +5036,7 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - + human clinical visit specified patient @@ -4779,15 +5057,9 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - An identifier that denotes a healthcare provider. - + + healthcare provider identifier @@ -4807,14 +5079,7 @@ It is not necessarily an immediate inpatient subsequent visit. - - - - - - - - + facility-supported clinical visit @@ -4847,8 +5112,6 @@ It is not necessarily an immediate inpatient subsequent visit. - - canadian facility address @@ -4866,7 +5129,7 @@ It is not necessarily an immediate inpatient subsequent visit. An information content entity that aims at representing the various forms of care provided within the healthcare organization clinical visit as approximated by a case-mix group definition. DRG - + diagnosis related group @@ -5218,18 +5481,6 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - identifier 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. Justin Whorton @@ -5258,12 +5509,6 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen @@ -5337,7 +5582,7 @@ When there is no such string, it is almost always because the entities take the Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. - + human birth statement @@ -5354,11 +5599,9 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - - A state sanctioned human birth statement. A state sanctioned human birth statement. - + civil birth record @@ -5383,7 +5626,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965Reese, Kyle died in 1984 A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human. - + human death statement @@ -5400,11 +5643,9 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - - A state sanctioned human death statement. A state sanctioned human death statement. - + civil death record @@ -5459,10 +5700,9 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - A biological sex information content entity that denotes the biological sex of a human. A biological sex information content entity that denotes the biological sex of a human. - + human biological sex information content entity @@ -5482,7 +5722,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 An information content entity that denotes a biological sex or a gender identity of a human. An information content entity that denotes a biological sex or a gender identity of a human. - + human biological sex or gender identity information content entity @@ -5503,16 +5743,10 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - - - - - - - 'Goose' (the name of a cat) An identifier that denotes a particular organism. An identifier that denotes a particular organism. + organism identifier @@ -5533,16 +5767,10 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - - - - - - - An organism identifier that denotes a particular human. An organism identifier that denotes a particular human. - + + human identifier @@ -5551,7 +5779,7 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - + @@ -5564,8 +5792,9 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - A statement stating the biological sex of a human. - A statement stating the biological sex of a human. + A pragmatically accepted statement stating the biological sex of a human. + A pragmatically accepted statement stating the biological sex of a human. + human biological sex statement @@ -5593,6 +5822,206 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 + + + + A pragmatically accepted statement that states characteristics of the primary residence of an individual at a given moment in time. + primary residence statement + + + + + + + + + An information content entity that aims at representing a type of living environment applicable to a primary residence. + living environment type + + + + + + + + + + + + 1 + + + + + Human birth date with data property + MPHPO human birth date + + + + + + + + + + + + 1 + + + + + human biological sex ICE with data property + MPHPO human biological sex information content entity + + + + + + + + + + + + 1 + + + + + ICU admission specification with data property + MPHPO ICU admission specification + + + + + + + + + + + + 1 + + + + + hospitalization admission urgency level specification with data property + MPHPO hospitalization admission urgency level specification + + + + + + + + + + + + 1 + + + + + healthcare physician service identifier with data property + MPHPO healthcare physician service identifier + + + + + + + + + + + + 1 + + + + + pathological condition impact type on clinical visit with data property + MPHPO pathological condition impact type on clinical visit + + + + + + + + + + + + 1 + + + + + pathological condition sub-group name with data property + MPHPO pathological condition sub-group name + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery beginning temporal information with data property + MPHPO healthcare organization service delivery beginning temporal information + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery ending temporal information with data property + MPHPO healthcare organization service delivery ending temporal information + + + + + + + + + + + + 1 + + + + + living environment type with data property + MPHPO living environment type + + + + @@ -5648,6 +6077,8 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965human human being + + Homo sapiens @@ -5668,17 +6099,6 @@ Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 - - - - - - - - - - - planned process planned process Injecting mice with a vaccine in order to test its efficacy @@ -5692,6 +6112,7 @@ objectives is a planned process. 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + planned process @@ -5808,7 +6229,6 @@ Updated: 2020-07-06 - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf @@ -5822,7 +6242,6 @@ Updated: 2020-07-06 - A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf @@ -5847,7 +6266,6 @@ Updated: 2020-07-06 - A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf @@ -5952,7 +6370,7 @@ edited date: 30 SEPT 2015 - + @@ -5963,14 +6381,14 @@ edited date: 30 SEPT 2015 Mathias Brochhausen facility - + - + 09/09/2017 @@ -5996,7 +6414,6 @@ edited date: 30 SEPT 2015 - A social identity information content entity that is about whether some person identifies as some gender. S. Clint Dowland @@ -6156,13 +6573,6 @@ edited date: 30 SEPT 2015 - - - - - - - An informational entity that fills an informational slot. An informational entity that fills an informational slot. informational filler @@ -6471,13 +6881,6 @@ edited date: 30 SEPT 2015 - - - - - - - - A planned process that aims at fulfilling the commitments of a service agreement. - A planned process that is maximally directed by a service agreement specification. @@ -6604,6 +7007,70 @@ edited date: 30 SEPT 2015 + + + + + + + + 1 + + + 4 Km + An information content entity whose structure and content follow a template. + specified value + + + + + + + + + numerical specified value + + + + + + + + + + + + 1 + + + + + + + 1 + + + + unit qualified scalar specified value + + + + + + + + + + + + + + + unit + + + + @@ -6639,28 +7106,14 @@ edited date: 30 SEPT 2015 - - - - - - - An information content entity that denotes a one-dimension temporal region. An information content entity that denotes a one-dimension temporal region. + temporal information - - - - root node - - - - @@ -6733,12 +7186,6 @@ The phrase "the pink elephant" describes an entity, but is not a &apos - - - - - - A Material Entity that is capable of performing Planned Acts http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology Agent @@ -7008,5 +7455,5 @@ The phrase "the pink elephant" describes an entity, but is not a &apos - + diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md index bab7587..0627a00 100644 --- a/docs/odk-workflows/ManageDocumentation.md +++ b/docs/odk-workflows/ManageDocumentation.md @@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to Just make sure you give GitHub 2-5 minutes to build the pages! + diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md index 2ca2064..9399509 100644 --- a/docs/odk-workflows/RepoManagement.md +++ b/docs/odk-workflows/RepoManagement.md @@ -2,7 +2,7 @@ ## Updating your ODK repository -Your ODK repositories configuration is managed in `src/ontology/RIDDLE-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository: +Your ODK repositories configuration is managed in `src/ontology/RIDDLE-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository: ``` diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 4b38ba2..bad7838 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -16,7 +16,7 @@ These are the current imports in RIDDLE | Import | URL | Type | | ------ | --- | ---- | -| HOSO | https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO-full.owl | mirror | +| HOSO | https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO.owl | mirror | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index c11bab0..dd61c80 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for RIDDLE # Generated using ontology-development-kit -# ODK Version: v1.4.3 +# ODK Version: v1.5.1 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use RIDDLE.Makefile instead @@ -9,6 +9,9 @@ # ---------------------------------------- # More information: https://github.com/INCATools/ontology-development-kit/ +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= 723d3ae4c095d804dcf5205d93dfa088ef18f9378f022b00b79db1bd3eefa34a + # ---------------------------------------- # Standard Constants @@ -41,9 +44,9 @@ REPORT_FAIL_ON = None REPORT_LABEL = -l true REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = -SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.3 +ODK_VERSION_MAKEFILE = v1.5.1 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -56,7 +59,12 @@ EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl FORMATS = $(sort owl owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) -RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base ) +RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base $(ONT)-non-classified ) + +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif # ---------------------------------------- # Top-level targets @@ -68,12 +76,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base ) all: all_odk .PHONY: all_odk -all_odk: odkversion test all_assets +all_odk: odkversion config_check test custom_reports all_assets .PHONY: test test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt echo "Finished running all tests successfully." +.PHONY: test +test_fast: + $(MAKE_FAST) test + .PHONY: release_diff release_diff: $(REPORTDIR)/release-diff.md @@ -84,13 +96,52 @@ reason_test: $(EDIT_PREPROCESSED) .PHONY: odkversion odkversion: - echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ - not the version of the ODK you are running)" &&\ - echo "ROBOT version (ODK): " && $(ROBOT) --version + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): mkdir -p $@ +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in RIDDLE.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -123,7 +174,7 @@ all_imports: $(IMPORT_FILES) # ---------------------------------------- -SUBSETS = RIDDLE_slim +SUBSETS = MPHPO-Slim SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) @@ -180,10 +231,10 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR) +sparql_test: $(EDIT_PREPROCESSED) | $(REPORTDIR) ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + $(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) endif # ---------------------------------------- @@ -196,6 +247,10 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri $(URIBASE)/RIDDLE_ --base-iri $(URIBASE)/RIDDLE --print 5 -o $@ +check_for_robot_updates: + echo "You are not using a custom profile, so you are getting the joy of the latest ROBOT report!" + + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -212,7 +267,7 @@ RELEASE_ASSETS = \ $(SUBSET_FILES) .PHONY: all_assets -all_assets: $(ASSETS) +all_assets: $(ASSETS) check_rdfxml_assets .PHONY: show_assets show_assets: @@ -220,7 +275,7 @@ show_assets: du -sh $(ASSETS) check_rdfxml_%: % - @check-rdfxml $< + @check-rdfxml $< .PHONY: check_rdfxml_assets check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) @@ -344,20 +399,24 @@ IMP=true # Global parameter to bypass import generation MIR=true # Global parameter to bypass mirror generation IMP_LARGE=true # Global parameter to bypass handling of large imports +ifeq ($(strip $(MIR)),true) ## ONTOLOGY: HOSO .PHONY: mirror-HOSO .PRECIOUS: $(MIRRORDIR)/HOSO.owl mirror-HOSO: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO-full.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) convert -I https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO.owl -o $(TMPDIR)/$@.owl $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) - if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi +else # MIR=false +$(MIRRORDIR)/%.owl: + @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." +endif @@ -397,7 +456,7 @@ endif # Release artefacts: main release artefacts # ---------------------------------------- -$(ONT).owl: $(ONT)-full.owl +$(ONT).owl: $(ONT)-non-classified.owl $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ convert -o $@.tmp.owl && mv $@.tmp.owl $@ @@ -415,9 +474,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) -# base: All the axioms as they are editted by the editors, excluding reasoning -$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) - $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri $(URIBASE)/RIDDLE --axioms external --preserve-structure false --trim false \ $(SHARED_ROBOT_COMMANDS) \ annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ @@ -429,6 +492,10 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) relax \ reduce -r ELK \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ +# foo-non-classified: (edit->imports-merged) +$(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ # ---------------------------------------- # Debugging Tools # ---------------------------------------- @@ -484,13 +551,16 @@ update_repo: update_docs: mkdocs gh-deploy --config-file ../../mkdocs.yaml -# Note to future generations: prepending ./ is a safety measure to ensure that -# the environment does not malicously set `CLEANFILES` to `\`. +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. .PHONY: clean clean: - [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* - [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* - [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done rm -f $(CLEANFILES) .PHONY: help @@ -509,6 +579,7 @@ Core commands: * prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. * update_repo: Update the ODK repository setup using the config file RIDDLE-odk.yaml * test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components * odkversion: Show the current version of the ODK Makefile and ROBOT. * clean: Delete all temporary files * help: Print ODK Usage information @@ -526,7 +597,7 @@ Imports management: Editor utilities: * validate_idranges: Make sure your ID ranges file is formatted correctly -* normalize_src: Load and safe your RIDDLE-edit file after you to make sure its serialised correctly +* normalize_src: Load and save your RIDDLE-edit file after you to make sure its serialised correctly * explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes * validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files * validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. diff --git a/src/ontology/RIDDLE-edit.owl b/src/ontology/RIDDLE-edit.owl index ff08046..28f7346 100644 --- a/src/ontology/RIDDLE-edit.owl +++ b/src/ontology/RIDDLE-edit.owl @@ -1,4 +1,3 @@ - Prefix(:=) Prefix(dce:=) Prefix(owl:=) @@ -9,37 +8,167 @@ Prefix(rdfs:=) Prefix(dcterms:=) -Ontology( - +Ontology( Import() - - -Annotation(dcterms:description "None") +Annotation(dcterms:description "Ontology for project RIDDLE"@en) Annotation(dcterms:license ) -Annotation(dcterms:title "RIDDLE project ontology") - - -Declaration(Class()) +Annotation(dcterms:title "Mortality Prediction for Hospitalized Patient Ontology"@en) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty(dcterms:description)) Declaration(AnnotationProperty(dcterms:license)) Declaration(AnnotationProperty(dcterms:title)) - +Declaration(Datatype()) ############################ # Annotation Properties ############################ +# Annotation Property: (MPHPO-Slim) + +AnnotationAssertion(rdfs:comment "Subset for RIDDLE project"@en) +AnnotationAssertion(rdfs:label "MPHPO-Slim"@en) +SubAnnotationPropertyOf( ) + +# Annotation Property: dcterms:description (description) + AnnotationAssertion(rdfs:label dcterms:description "description") + +# Annotation Property: dcterms:license (license) + AnnotationAssertion(rdfs:label dcterms:license "license") + +# Annotation Property: dcterms:title (title) + AnnotationAssertion(rdfs:label dcterms:title "title") + + ############################ -# Classes +# Datatypes ############################ -# Class: (root node) +# Datatype: (ISO8601 DateTime) -AnnotationAssertion(rdfs:label "root node"@en) +AnnotationAssertion(rdfs:label "ISO8601 DateTime"@en) -) +############################ +# Classes +############################ +# Class: (MPHPO human birth date) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Human birth date with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO human birth date"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 )) + +# Class: (MPHPO human biological sex information content entity) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "human biological sex ICE with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO human biological sex information content entity"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO ICU admission specification) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "ICU admission specification with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO ICU admission specification"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO hospitalization admission urgency level specification) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "hospitalization admission urgency level specification with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO hospitalization admission urgency level specification"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO healthcare physician service identifier) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "healthcare physician service identifier with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO healthcare physician service identifier"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO pathological condition impact type on clinical visit) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "pathological condition impact type on clinical visit with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO pathological condition impact type on clinical visit"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO pathological condition sub-group name) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "pathological condition sub-group name with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO pathological condition sub-group name"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + +# Class: (MPHPO healthcare organization service delivery beginning temporal information) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "healthcare organization service delivery beginning temporal information with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO healthcare organization service delivery beginning temporal information"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 )) + +# Class: (MPHPO healthcare organization service delivery ending temporal information) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "healthcare organization service delivery ending temporal information with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO healthcare organization service delivery ending temporal information"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 )) + +# Class: (MPHPO living environment type) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "living environment type with data property"@en) +AnnotationAssertion(rdfs:label "MPHPO living environment type"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 xsd:string)) + + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +) \ No newline at end of file diff --git a/src/ontology/RIDDLE-odk.yaml b/src/ontology/RIDDLE-odk.yaml index cc39415..8e80ab1 100644 --- a/src/ontology/RIDDLE-odk.yaml +++ b/src/ontology/RIDDLE-odk.yaml @@ -1,5 +1,5 @@ id: RIDDLE -title: RIDDLE project ontology +title: Mortality Prediction for Hospitalized Patient github_org: OpenLHS repo: RIDDLE documentation: @@ -7,15 +7,16 @@ documentation: release_artefacts: - full - base -primary_release: full + - non-classified +primary_release: non-classified export_formats: - owl import_group: products: - id: HOSO module_type: mirror - mirror_from: "https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO-full.owl" + mirror_from: "https://raw.githubusercontent.com/OpenLHS/HOSO/main/HOSO.owl" subset_group: products: - - id: RIDDLE_slim + - id: MPHPO-Slim robot_java_args: "-Xmx8G" \ No newline at end of file diff --git a/src/ontology/imports/HOSO_import.owl b/src/ontology/imports/HOSO_import.owl index 8439320..4a025f5 100644 --- a/src/ontology/imports/HOSO_import.owl +++ b/src/ontology/imports/HOSO_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-10-12") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-02") Declaration(Class()) Declaration(Class()) @@ -132,6 +132,21 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -180,6 +195,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -233,6 +250,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -313,6 +334,11 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -342,10 +368,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -492,26 +515,11 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) -# Annotation Property: (HEPRO-H) +# Annotation Property: (OpenLHS-H) -AnnotationAssertion(rdfs:label "HEPRO-H"@en) -SubAnnotationPropertyOf( ) - -# Annotation Property: (HOSO-H) - -AnnotationAssertion(rdfs:comment "HOSO classes relevant to humans."@en) -AnnotationAssertion(rdfs:label "HOSO-H"@en) -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (IOIO-H) - -AnnotationAssertion(rdfs:comment "IOIO classes relevent to humans."@en) -AnnotationAssertion(rdfs:label "IOIO-H"@en) -SubAnnotationPropertyOf( ) +AnnotationAssertion(rdfs:comment "OpenLHS classes relevant to humans."@en) +AnnotationAssertion(rdfs:label "OpenLHS-H"@en) +SubAnnotationPropertyOf( ) # Annotation Property: () @@ -1374,6 +1382,36 @@ ObjectPropertyDomain( ) +############################ +# Data Properties +############################ + +# Data Property: (has textual representation) + +AnnotationAssertion(rdfs:label "has textual representation"@en) +SubDataPropertyOf( owl:topDataProperty) + +# Data Property: (has value) + +AnnotationAssertion(rdfs:label "has value"@en) +SubDataPropertyOf( owl:topDataProperty) + +# Data Property: (has numerical value) + +AnnotationAssertion(rdfs:label "has numerical value"@en) +SubDataPropertyOf( ) + +# Data Property: (has temporal value) + +AnnotationAssertion(rdfs:label "has temporal value"@en) +SubDataPropertyOf( ) + +# Data Property: (has text value) + +AnnotationAssertion(rdfs:label "has text value"@en) +SubDataPropertyOf( ) + + ############################ # Classes @@ -1973,15 +2011,15 @@ SubClassOf( "A request requesting the execution of some health procedure."@en) AnnotationAssertion( "A request that has as part a health procedure specification."@en) AnnotationAssertion( "A request requesting the execution of some health procedure."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health procedure request"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (health procedure report) AnnotationAssertion( "An information content entity containing information about some health procedure requests and possibly the associated health procedures."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health procedure report"@en) SubClassOf( ) @@ -1992,25 +2030,23 @@ AnnotationAssertion( "A planned process that has some components that are planned processes, including at least one that is a health activity."@en) AnnotationAssertion( "- A planned process that is maximally directed by a health procedure specification. - A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health procedure"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (health activity) AnnotationAssertion( "A planned process that aims to produce a truthful statement about the health status of an organism or modify it."@en) AnnotationAssertion( "A planned process that aims to produce a truthful statement about the health status of an organism or modify it."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health activity"@en) SubClassOf( ) # Class: (health procedure resulting process) AnnotationAssertion( "A planned process that is a part of a health procedure, that has as specified input at least one health activity outcome information and aim at generating a health procedure outcome information."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health procedure resulting process"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2018,7 +2054,7 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (health procedure outcome information) AnnotationAssertion( "An information content entity that is the output of a health procedure resulting process and that describes some outcomes of a health procedure."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health procedure outcome information"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2027,7 +2063,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion( "An information content entity that is a specified output of a health activity."@en) AnnotationAssertion( "An information content entity that is a specified output of a health activity."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health activity outcome information"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2035,24 +2071,25 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (health provider identifier) AnnotationAssertion( "An individual identifier that denotes a health provider."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health provider identifier"@en) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectExactCardinality(1 )) # Class: (physician identifier) AnnotationAssertion( "A health provider identifier that is used to denote a person authorised to act as a physician."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "physician identifier"@en) SubClassOf( ) +SubClassOf( ObjectExactCardinality(1 )) # Class: (health provider role) AnnotationAssertion( "A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities."@en) AnnotationAssertion( "This usually includes health professional like physicians, nurses or pharmacists etc. It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health provider role"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2060,22 +2097,22 @@ SubClassOf( ObjectSomeValuesFrom(< # Class: (health provider) AnnotationAssertion( "An organism that is the bearer of a health provider role."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "health provider"@en) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (diagnostic health procedure) -AnnotationAssertion( "TBD"@en) -AnnotationAssertion( ) +AnnotationAssertion( "A health procedure that include a diagnostic procedure - TBD."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diagnostic health procedure"@en) SubClassOf( ) # Class: (surgical health procedure) -AnnotationAssertion( "TBD"@en) -AnnotationAssertion( ) +AnnotationAssertion( "A health procedure that includes a surgical procedure - TBD."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "surgical health procedure"@en) SubClassOf( ) @@ -2247,7 +2284,7 @@ SubClassOf( ObjectSomeValuesFrom( (healthcare facility) -AnnotationAssertion( "TBD"@en) +AnnotationAssertion( "A facility that bears a healthcare function - WiP."@en) AnnotationAssertion(rdfs:label "healthcare facility"@en) SubClassOf( ) @@ -2269,8 +2306,6 @@ SubClassOf( ObjectSomeValuesFrom( "A health provider who is a member of a healthcare organisation."@en) AnnotationAssertion(rdfs:label "healthcare provider"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (healthcare procedure) @@ -2282,7 +2317,7 @@ SubClassOf( ObjectSomeValuesFrom( (healthcare organization service delivery) AnnotationAssertion( "A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare organization service delivery"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2290,56 +2325,56 @@ SubClassOf( ObjectSomeValuesFrom( (healthcare organization clinical visit) AnnotationAssertion( "A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare organization clinical visit"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectExactCardinality(1 )) # Class: (ancillary care service delivery) AnnotationAssertion( "A service delivery that aims to support health services without directly providing a desired effect on the health status of individuals or communities."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ancillary care service delivery"@en) SubClassOf( ) # Class: (custodial care service delivery) AnnotationAssertion( "A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "custodial care service delivery"@en) SubClassOf( ) # Class: (populational healthcare service) AnnotationAssertion( "A healthcare service that aims at providing a desired effect on the health status of a community."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "populational healthcare service"@en) SubClassOf( ) # Class: (healthcare organization clinical encounter) AnnotationAssertion( "A temporally-connected healthcare organization clinical visit that aims to improve, maintain or restore the health of some participating organism."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare organization clinical encounter"@en) SubClassOf( ) # Class: (facility-supported healthcare encounter) AnnotationAssertion( "A healthcare encounter during which the recipient is located in a healthcare facility at some time."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facility-supported healthcare encounter"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (public provincial health identifier) AnnotationAssertion( "An identifier that denotes a public provincial health insurance record."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "public provincial health identifier"@en) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (healthcare facility identifier) @@ -2358,29 +2393,31 @@ SubClassOf( ObjectExactCardinality( # Class: (outpatient visit) AnnotationAssertion( "A healthcare organisation clinical visit where the patient physically attends to a healthcare facility, but where there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outpatient visit"@en) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inpatient visit) AnnotationAssertion( "A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inpatient visit"@en) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (day inpatient visit) AnnotationAssertion( "An inpatient visit that does not extend overnight."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "day inpatient visit"@en) SubClassOf( ) # Class: (day inpatient surgery visit) AnnotationAssertion( "A day inpatient visit which includes a surgical procedure."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "day inpatient surgery visit"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2388,7 +2425,7 @@ SubClassOf( ObjectSomeValuesFrom( (hospitalization) AnnotationAssertion( "An inpatient visit located in a hospital facility requested by a physician, that may extends overnight."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hospitalization"@en) SubClassOf( ) @@ -2396,48 +2433,46 @@ SubClassOf( "A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. It is not necessarily an immediate inpatient subsequent visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "emergency department visit"@en) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (emergency department inpatient visit) AnnotationAssertion( "An emergency department visit and an inpatient visit, where there is usually limited accommodation and where the goal is to stabilise a life-threatening condition or decide whether the clinical situation requires a hospitalisation visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "emergency department inpatient visit"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) # Class: (emergency department outpatient visit) AnnotationAssertion( "An emergency department visit and an outpatient visit."@en) -AnnotationAssertion( "there is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient"@en) -AnnotationAssertion( ) +AnnotationAssertion( "There is no expectation of providing support for activities of daily living (such as eating and bathing) nor accommodation for the patient"@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "emergency department outpatient visit"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (walk-in clinic visit) -AnnotationAssertion( "an outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions"@en) -AnnotationAssertion( ) +AnnotationAssertion( "An outpatient visit where there is expectation of providing unplanned, timely care, but excluding handling life-threatening conditions."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "walk-in clinic visit"@en) SubClassOf( ) # Class: (outpatient surgery visit) -AnnotationAssertion( "an outpatient visit which includes a surgical procedure"@en) -AnnotationAssertion( ) +AnnotationAssertion( "An outpatient visit which includes a surgical procedure."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outpatient surgery visit"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (outpatient diagnostic visit) -AnnotationAssertion( "an outpatient visit which includes a diagnostic procedure"@en) -AnnotationAssertion( ) +AnnotationAssertion( "An outpatient visit which includes a diagnostic procedure."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "outpatient diagnostic visit"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2445,16 +2480,14 @@ SubClassOf( ObjectSomeValuesFrom( (immediate inpatient subsequent visit) AnnotationAssertion( "An immediate subsequent visit healthcare organisation visit for a given patient that was participating in another healthcare organisation visit for the same organisation just prior to this visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immediate inpatient subsequent visit"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) # Class: (prior visit category to an inpatient visit) AnnotationAssertion( "An information content entity describing the type of visit that occured prior to an immediate inpatient subsequent visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prior visit category to an inpatient visit"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) @@ -2462,7 +2495,7 @@ SubClassOf( ObjectSomeValuesFrom( (still born healthcare service) AnnotationAssertion( "A healthcare organisation service delivery where the main entity of interest is a still born."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "still born healthcare service"@en) SubClassOf( ) @@ -2470,33 +2503,31 @@ SubClassOf( "A healthcare organization clinical visit during which a birth statement was produced regarding the birth of the main patient visit beneficiary."@en) AnnotationAssertion( "In the case of human health the specified organism refers to the child born during the visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare birth visit"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectExactCardinality(1 ))))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectExactCardinality(1 )))) # Class: (inpatient visit from an external location) AnnotationAssertion( "Patient hospitalized directly from home."@en) AnnotationAssertion( "Patient transferred from a healthcare organization emergency department to be hospitalized by a different healthcare organization."@en) AnnotationAssertion( "an inpatient visit that is not immedately following another healthcare organisation clinical visit in the same organisation, and is not a healthcare birth visit"@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inpatient visit from an external location"@en) SubClassOf( ) # Class: (ambulance initiated emergency department visit) AnnotationAssertion( "An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( "Considérer axomatisation séquentielle") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ambulance initiated emergency department visit"@en) -SubClassOf( ) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cadaver service) AnnotationAssertion( "A healthcare organization service delivery where the main entity of interest is a human cadaver that was not delivered just prior to this service."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cadaver service"@en) SubClassOf( ) @@ -2504,16 +2535,14 @@ SubClassOf( "A healthcare organization clinical visit during which a death statement was produced regarding the death of the main patient visit beneficiary."@en) AnnotationAssertion( "A healthcare organization clinical visit during which the patient died."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare visit of expiration"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectExactCardinality(1 ))))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectExactCardinality(1 )))) # Class: (visit discharge specification) AnnotationAssertion( "A directive information entity that aims at directing what health procedures or healthcare organization services are recommended after this visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit discharge specification"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2521,7 +2550,7 @@ SubClassOf( ObjectSomeValuesFrom( (visit transfer specification) AnnotationAssertion( "A visit discharge specification that aims at directing to which healthcare organisation the patient should be transferred after the end of the current visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit transfer specification"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2529,7 +2558,7 @@ SubClassOf( ObjectSomeValuesFrom( (visit transfer specification category) AnnotationAssertion( "An information content entity that is part of a visit transfer specification and is about the type of healthcare organization specified."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit transfer specification category"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2537,37 +2566,35 @@ SubClassOf( ObjectSomeValuesFrom( (visit discharge specification for home) AnnotationAssertion( "A visit discharge specification for a given clinical visit that has no visit transfer specification."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit discharge specification for home"@en) EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) -SubClassOf( ) # Class: (visit ended by the patient) AnnotationAssertion( "A healthcare organization clinical visit ended at the initiative of the patient without physician approval."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit ended by the patient"@en) EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) -SubClassOf( ) # Class: (visit ended by the patient without notification) AnnotationAssertion( "A visit ended by the patient without notifying the healthcare organization."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit ended by the patient without notification"@en) SubClassOf( ) # Class: (triage-only emergency department visit) AnnotationAssertion( "An emergency department visit with a triage encounter but no further encounter."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "triage-only emergency department visit"@en) SubClassOf( ) # Class: (emergency department visit with partial treatment) AnnotationAssertion( "An emergency department visit and a visit ended by the patient and some treatment healthcare procedure was provided."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "emergency department visit with partial treatment"@en) SubClassOf( ) SubClassOf( ) @@ -2576,7 +2603,7 @@ SubClassOf( "An identifier that denotes a diagnosis related group."@en) AnnotationAssertion( "DRG code"@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "visit diagnosis related group code"@en) SubClassOf( ) @@ -2584,7 +2611,7 @@ SubClassOf( "A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery."@en) AnnotationAssertion( "A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare organization service delivery beginning statement"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2594,7 +2621,7 @@ SubClassOf( ObjectSomeValuesFrom( "A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery."@en) AnnotationAssertion( "A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare organization service delivery ending statement"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -2603,7 +2630,7 @@ SubClassOf( ObjectSomeValuesFrom( (public provincial health insurance record) AnnotationAssertion( "An information content entity that contains the information required to manage the insurance coverage of an insured individual."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "public provincial health insurance record"@en) SubClassOf( ) SubClassOf( ObjectExactCardinality(1 )) @@ -2620,7 +2647,6 @@ AnnotationAssertion( "primary health insurance beneficiary human"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (public provincial health insurance primary residence statement) @@ -2639,25 +2665,124 @@ SubClassOf( ObjectSomeValuesFrom( (immediate subsequent visit) AnnotationAssertion( "A healthcare organization clinical visit for a given patient that was participating in another healthcare organisation clinical visit just prior to this visit."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immediate subsequent visit"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (immediate subsequent visit in same organization) AnnotationAssertion( "An immediate subsequent visit where both visits are under the responsability of the same healthcare organisation."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immediate subsequent visit in same organization"@en) SubClassOf( ) +# Class: (direct ambulance initiated hospitalization) + +AnnotationAssertion( "An hospitalization for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit."@en) +AnnotationAssertion(rdfs:label "direct ambulance initiated hospitalization"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (ambulance paramedics visit) + +AnnotationAssertion( "A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider."@en) +AnnotationAssertion(rdfs:label "ambulance paramedics visit"@en) +SubClassOf( ) + +# Class: (ED by ambulance initiated hospitalization) + +AnnotationAssertion( "An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit."@en) +AnnotationAssertion(rdfs:label "ED by ambulance initiated hospitalization"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (ICU admission specification) + +AnnotationAssertion( "A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit."@en) +AnnotationAssertion(rdfs:label "ICU admission specification"@en) +SubClassOf( ) + +# Class: (clinical visit agreement specification) + +AnnotationAssertion( "A service agreement specification for a clinical visit admission."@en) +AnnotationAssertion(rdfs:label "clinical visit agreement specification"@en) +SubClassOf( ) + +# Class: (clinical visit urgency level specification) + +AnnotationAssertion( "A clinical visit agreement specification mandating the urgency level of the clinical visit."@en) +AnnotationAssertion(rdfs:label "clinical visit urgency level specification"@en) +SubClassOf( ) + +# Class: (hospitalization admission urgency level specification) + +AnnotationAssertion( "A clinical visit urgency level specification mandating the urgency level of the hospitalization admission."@en) +AnnotationAssertion(rdfs:label "hospitalization admission urgency level specification"@en) +SubClassOf( ) + +# Class: (clinical visit unit type specification) + +AnnotationAssertion( "A clinical visit agreement specification mandating the type of unit required for a clinical visit."@en) +AnnotationAssertion(rdfs:label "clinical visit unit type specification"@en) +SubClassOf( ) + +# Class: (hospitalization admitting physician specification) + +AnnotationAssertion( "A clinical visit agreement specification mandating the admitting physician."@en) +AnnotationAssertion(rdfs:label "hospitalization admitting physician specification"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (healthcare physician service) + +AnnotationAssertion( "A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members"@en) +AnnotationAssertion(rdfs:comment "It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department."@en) +AnnotationAssertion(rdfs:comment "It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon)."@en) +AnnotationAssertion(rdfs:label "healthcare physician service"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (living environment type prior to clinical visit statement) + +AnnotationAssertion( "A primary residence statement that states the type of living environment of a patient immediately prior to a clinical visit."@en) +AnnotationAssertion(rdfs:label "living environment type prior to clinical visit statement"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (patient) + +AnnotationAssertion( "An eukaryote that is the bearer of a patient role."@en) +AnnotationAssertion(rdfs:label "patient"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (patient role) + +AnnotationAssertion( "A role born by an organism which is the primary recipient in a healthcare organization clinical visit."@en) +AnnotationAssertion(rdfs:label "patient role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (human patient) + +AnnotationAssertion( "A patient that is a Homo sapiens."@en) +AnnotationAssertion(rdfs:label "human patient"@en) +EquivalentClasses( ObjectIntersectionOf( )) + +# Class: (healthcare physician service identifier) + +AnnotationAssertion( "A healthcare organization identifier that denotes a physician service."@en) +AnnotationAssertion(rdfs:label "healthcare physician service identifier"@en) +SubClassOf( ) +SubClassOf( ObjectExactCardinality(1 )) + # Class: (healthcare organization service delivery identifier) AnnotationAssertion( "An identifier that denotes a healthcare organization service delivery."@en) AnnotationAssertion( "An identifier that denotes a healthcare organization service delivery."@en) AnnotationAssertion(rdfs:label "healthcare organization service delivery identifier"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (healthcare organization service delivery beginning temporal information) @@ -2665,6 +2790,7 @@ AnnotationAssertion( "A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery."@en) AnnotationAssertion(rdfs:label "healthcare organization service delivery beginning temporal information"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (healthcare organization service delivery ending temporal information) @@ -2707,6 +2833,7 @@ AnnotationAssertion( "A pragmatically accepted statement that states the impact of a pathological condition on a clinical visit."@en) AnnotationAssertion(rdfs:label "health organization clinical visit pathological condition impact statement"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -2727,25 +2854,19 @@ SubClassOf( "human clinical visit specified patient"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (healthcare provider identifier) AnnotationAssertion( "An identifier that denotes a healthcare provider."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "healthcare provider identifier"@en) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (facility-supported clinical visit) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "facility-supported clinical visit"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (facility address) @@ -2758,14 +2879,12 @@ SubClassOf( ObjectSomeValuesFrom( "canadian facility address"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) # Class: (diagnosis related group) AnnotationAssertion( "An information content entity that aims at representing the various forms of care provided within the healthcare organization clinical visit as approximated by a case-mix group definition."@en) AnnotationAssertion( "DRG"@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "diagnosis related group"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -3010,8 +3129,6 @@ AnnotationAssertion(rdfs:comment "S AnnotationAssertion(rdfs:label "identifier"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (identifier creating process) @@ -3025,7 +3142,6 @@ AnnotationAssertion( "identifier creating process"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (code set) @@ -3065,7 +3181,7 @@ AnnotationAssertion( "A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human."@en) AnnotationAssertion( "A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human birth statement"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -3075,18 +3191,16 @@ SubClassOf( ObjectSomeValuesFrom( "A state sanctioned human birth statement."@en) AnnotationAssertion( "A state sanctioned human birth statement."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "civil birth record"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) # Class: (human death statement) AnnotationAssertion( "Reese, Kyle died in 1984"@en) AnnotationAssertion( "A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human."@en) AnnotationAssertion( "A process temporally qualifying statement about the death of a human including an identifier and a temporal information of the death of this human."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human death statement"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -3096,11 +3210,9 @@ SubClassOf( ObjectSomeValuesFrom( "A state sanctioned human death statement."@en) AnnotationAssertion( "A state sanctioned human death statement."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "civil death record"@en) EquivalentClasses( ObjectIntersectionOf( )) -SubClassOf( ) -SubClassOf( ) # Class: (human birth temporal information) @@ -3129,16 +3241,15 @@ SubClassOf( "A biological sex information content entity that denotes the biological sex of a human."@en) AnnotationAssertion( "A biological sex information content entity that denotes the biological sex of a human."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human biological sex information content entity"@en) SubClassOf( ) -SubClassOf( ) # Class: (human biological sex or gender identity information content entity) AnnotationAssertion( "An information content entity that denotes a biological sex or a gender identity of a human."@en) AnnotationAssertion( "An information content entity that denotes a biological sex or a gender identity of a human."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human biological sex or gender identity information content entity"@en) EquivalentClasses( ObjectUnionOf( )) SubClassOf( ) @@ -3150,25 +3261,22 @@ AnnotationAssertion( "An identifier that denotes a particular organism."@en) AnnotationAssertion(rdfs:label "organism identifier"@en) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (human identifier) AnnotationAssertion( "An organism identifier that denotes a particular human."@en) AnnotationAssertion( "An organism identifier that denotes a particular human."@en) -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human identifier"@en) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (human biological sex statement) -AnnotationAssertion( "A statement stating the biological sex of a human."@en) -AnnotationAssertion( "A statement stating the biological sex of a human."@en) +AnnotationAssertion( "A pragmatically accepted statement stating the biological sex of a human."@en) +AnnotationAssertion( "A pragmatically accepted statement stating the biological sex of a human."@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "human biological sex statement"@en) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -3186,6 +3294,18 @@ AnnotationAssertion( "human death date"@en) SubClassOf( ) +# Class: (primary residence statement) + +AnnotationAssertion( "A pragmatically accepted statement that states characteristics of the primary residence of an individual at a given moment in time."@en) +AnnotationAssertion(rdfs:label "primary residence statement"@en) +SubClassOf( ) + +# Class: (living environment type) + +AnnotationAssertion( "An information content entity that aims at representing a type of living environment applicable to a primary residence."@en) +AnnotationAssertion(rdfs:label "living environment type"@en) +SubClassOf( ) + # Class: (Viruses) AnnotationAssertion( "Viruses") @@ -3223,6 +3343,7 @@ AnnotationAssertion( "human") AnnotationAssertion( "human being") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Homo sapiens") SubClassOf( ) @@ -3244,7 +3365,6 @@ AnnotationAssertion( "planned process"@en) EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) # Class: (organization) @@ -3336,7 +3456,6 @@ AnnotationAssertion( "creation date: 2009-06-23T11:21:20Z") AnnotationAssertion(rdfs:label "disease") SubClassOf( ) -SubClassOf( ) # Class: (disorder) @@ -3346,7 +3465,6 @@ AnnotationAssertion( "creation date: 2009-06-23T11:39:44Z") AnnotationAssertion(rdfs:label "disorder") SubClassOf( ) -SubClassOf( ) # Class: (bodily process) @@ -3363,7 +3481,6 @@ AnnotationAssertion( "creation date: 2009-06-23T11:54:29Z") AnnotationAssertion(rdfs:label "pathological bodily process") SubClassOf( ) -SubClassOf( ) # Class: (syndrome) @@ -3454,7 +3571,6 @@ AnnotationAssertion( "Sarah Bost"@en) AnnotationAssertion( "William R. Hogan"@en) AnnotationAssertion(rdfs:label "gender identity information content entity"@en) -SubClassOf( ) SubClassOf( ) # Class: (female gender identity information content entity) @@ -3531,8 +3647,6 @@ AnnotationAssertion( "An informational entity that fills an informational slot."@en) AnnotationAssertion(rdfs:label "informational filler"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (canadian postal address) @@ -3665,8 +3779,6 @@ AnnotationAssertion(Annotation(rdfs:comment "All service deliveries are directed - A planned process that is maximally directed by a service agreement specification."@en) AnnotationAssertion(rdfs:label "service delivery"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (agent plan to act as if some statement was true) @@ -3716,6 +3828,32 @@ AnnotationAssertion( "continuant disappearance statement"@en) SubClassOf( ) +# Class: (specified value) + +AnnotationAssertion( "4 Km"@en) +AnnotationAssertion( "An information content entity whose structure and content follow a template."@en) +AnnotationAssertion(rdfs:label "specified value"@en) +SubClassOf( ) +SubClassOf( DataExactCardinality(1 )) + +# Class: (numerical specified value) + +AnnotationAssertion(rdfs:label "numerical specified value"@en) +SubClassOf( ) + +# Class: (unit qualified scalar specified value) + +AnnotationAssertion(rdfs:label "unit qualified scalar specified value"@en) +SubClassOf( ) +SubClassOf( ObjectExactCardinality(1 )) +SubClassOf( ObjectExactCardinality(1 )) + +# Class: (unit) + +AnnotationAssertion(rdfs:label "unit"@en) +SubClassOf( ) +SubClassOf( DataSomeValuesFrom( xsd:string)) + # Class: (pathological condition) AnnotationAssertion( "An entity that is a disorder, a disease or a pathological bodily process"@en) @@ -3730,8 +3868,6 @@ AnnotationAssertion( "An information content entity that denotes a one-dimension temporal region."@en) AnnotationAssertion(rdfs:label "temporal information"@en) EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(1 ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (statement) @@ -3779,7 +3915,6 @@ AnnotationAssertion( "Agent"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (Agent Capability) diff --git a/src/ontology/run.sh b/src/ontology/run.sh index 2718ff6..873e9bd 100644 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -14,6 +14,8 @@ # # See README-editors.md for more details. +set -e + if [ -f run.sh.conf ]; then . ./run.sh.conf fi @@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") fi +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + ODK_IMAGE=${ODK_IMAGE:-odkfull} TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') if [ -n "$TAG_IN_IMAGE" ]; then @@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest} ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} ODK_DEBUG=${ODK_DEBUG:-no} +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + TIMECMD= if [ x$ODK_DEBUG = xyes ]; then # If you wish to change the format string, take care of using # non-breaking spaces (U+00A0) instead of normal spaces, to # prevent the shell from tokenizing the format string. - echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" fi +rm -f tmp/debug.log -VOLUME_BIND=$PWD/../../:/work +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND WORK_DIR=/work/src/ontology if [ -n "$ODK_BINDS" ]; then @@ -59,14 +89,14 @@ fi if [ -n "$USE_SINGULARITY" ]; then singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ - --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ --bind $VOLUME_BIND \ -W $WORK_DIR \ docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" else BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ - -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" fi diff --git a/src/ontology/subsets/MPHPO-Slim.owl b/src/ontology/subsets/MPHPO-Slim.owl new file mode 100644 index 0000000..9a906e0 --- /dev/null +++ b/src/ontology/subsets/MPHPO-Slim.owl @@ -0,0 +1,4065 @@ + + + + + 2024-08-02 + + + + + + + + + + + + + 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 + + + + + + + + + example of usage + + + + + + + + + + + + + + + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + curator note + + + + + + + + + + + + + + + imported from + + + + + + + + + elucidation + + + + + + + + + has associated axiom(nl) + + + + + + + + + has associated axiom(fol) + + + + + + + + + has axiom label + + + + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary conditions + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary conditions associated with an entity, we write as definitional necessary condition the conjunction of them. + + + + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary and sufficient conditions + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary and sufficient conditions associated with an entity, we regroup them in the same annotation. + + + + + + + + Human-readable necessary membership condition(s) of a class or a property. + We introduce 'necessary conditions' rather than 'necessary condition' to avoid the multiplication of annotations. + necessary conditions + + + + + + + + Human-readable necessary and sufficient membership conditions of a class or a property. + necessary and sufficient conditions + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subset for RIDDLE project + MPHPO-Slim + + + + + + + + + OpenLHS classes relevant to humans. + OpenLHS-H + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ISO8601 DateTime + + + + + + + + + + + + + + + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 + + + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + TBD + has participating performer + + + + + + + + + TBD + has participating recipient + + + + + + + + + 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 + + + + + + + + Inverse of the relation 'mentions' + + + 2022-01-28T07:20:08Z + mentioned by + + + + + + + + + + + + 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 + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + The inverse property of is_specified_input_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 + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + 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. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + The inverse property of is_specified_output_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 + + + + + + + + + is administered by + + + + + + + + + + + A relation that holds between a filler and a slot it fills. + fills + + + + + + + + + + + The inverse relations of directs + The inverse relations of directs + is directed by + + + + + + + + + + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + is about an aspect of + + + + + + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + A directs B := A is a directive information entity that guides an agent in the execution of B. + directs + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + This includes failed attempts where B is not compliant to A. + + + + + + + + + + The inverse relation of fills + The inverse relation of fills + is filled by + + + + + + + + + + + A maximally directs B := A directs B, and B is compliant to A. + A maximally directs B := A directs B, and B is compliant to A. + Discussed in: Adrien Barton, Laure Vieu, Jean-François Ethier. Directing Actions. Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), Sep 2019, Graz, Austria. + maximally directs + + + + + + + + + + + The inverse relation of maximally directs. + The inverse relation of maximally directs. + is maximally directed by + + + + + + + + + + The inverse relation of has component. + The inverse relation of has component. + component of + + + + + + + + + + + + The inverse relation of has component process. + The inverse relation of has component process. + component process of + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic + + + + + + + + + + + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + + 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 + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + + x agent_in y iff y is an instance of Process and x is an instance of Agent, such that x is causally active in y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + agent in + + + + + + + + + x has_agent y iff x is an instance of Process and y is an instance of Agent, such that y is causally active in x. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has agent + + + + + + + + + x has_capability y iff x is an instance of Agent and y is an instance of Agent Capability, such that x bearer of y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has capability + + + + + + + + + + + + + + has textual representation + + + + + + + + + has value + + + + + + + + + has numerical value + + + + + + + + + has temporal value + + + + + + + + + has text value + + + + + + + + + + + + + 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 + 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 + 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 + 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] + + + + + + + + + + + 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] + + + + + + + + + + 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. + 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 + + + + + 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 + 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] + + + + + + + + + + + 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 + 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 + 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. + 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 + + + + + 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] + + + + + + + + + + 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. + 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] + + + + + + + + + + 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 + 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 + + + + + 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] + + + + + + + + + + + + + + + + + + + + + + + + + + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + A planned process that has some components that are planned processes, including at least one that is a health activity. + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + + + health procedure + + + + + + + + + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + + health activity + + + + + + + + + + + + 1 + + + + An individual identifier that denotes a health provider. + + + health provider identifier + + + + + + + + + + + + + + + A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities. + This usually includes health professional like physicians, nurses or pharmacists etc. +It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants. + + health provider role + + + + + + + + + + + + + + + An organism that is the bearer of a health provider role. + + + health provider + + + + + + + + + + + + + + + An information content entity that is about a sub-group of pathological conditions. + We suppose that if an ICE is about a group of particular entities, it is also about each of these entities. + pathological condition sub-group name + + + + + + + + + A directive information entity that aims to direct a health procedure. + A directive information entity that aims to direct a health procedure. + + health procedure specification + + + + + + + + + + + + + + + A service agreement specification identifying an organism for whom a healthcare service delivery aims at providing a desired effect to its health status. + + healthcare service organism specification + + + + + + + + + A facility that bears a healthcare function - WiP. + healthcare facility + + + + + + + + + A role that inheres in an organisation and is realized by providing some healthcare service delivery. + healthcare organization role + + + + + + + + + + + + + + + An organisation that bears a healthcare organisation role. + healthcare organization + + + + + + + + + + + + + + + + + + + A health provider who is a member of a healthcare organisation. + + healthcare provider + + + + + + + + + + + + + + + A health procedure that is part of a healthcare service delivery and that is performed by a healthcare worker while realizing its health care worker role. + healthcare procedure + + + + + + + + + + + + + + + A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization. + + + healthcare organization service delivery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes. + + + healthcare organization clinical visit + + + + + + + + + A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities. + + custodial care service delivery + + + + + + + + + + + + 1 + + + + An identifier that denotes a healthcare organization. + healthcare organization identifier + + + + + + + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient. + + inpatient visit + + + + + + + + + An inpatient visit located in a hospital facility requested by a physician, that may extends overnight. + + + hospitalization + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. +It is not necessarily an immediate inpatient subsequent visit. + + + emergency department visit + + + + + + + + + + + + + + + + + + + An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + Considérer axomatisation séquentielle + + + ambulance initiated emergency department visit + + + + + + + + + + + + + + + + + + + + + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + + + healthcare organization service delivery beginning statement + + + + + + + + + + + + + + + + + + + + + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + + + healthcare organization service delivery ending statement + + + + + + + + + A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider. + + ambulance paramedics visit + + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit. + + ED by ambulance initiated hospitalization + + + + + + + + + A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit. + ICU admission specification + + + + + + + + + A service agreement specification for a clinical visit admission. + clinical visit agreement specification + + + + + + + + + A clinical visit agreement specification mandating the urgency level of the clinical visit. + clinical visit urgency level specification + + + + + + + + + A clinical visit urgency level specification mandating the urgency level of the hospitalization admission. + hospitalization admission urgency level specification + + + + + + + + + A clinical visit agreement specification mandating the type of unit required for a clinical visit. + clinical visit unit type specification + + + + + + + + + + + + + + + A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members + It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department. + It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon). + healthcare physician service + + + + + + + + + + + + + + + An eukaryote that is the bearer of a patient role. + patient + + + + + + + + + + + + + + + A role born by an organism which is the primary recipient in a healthcare organization clinical visit. + patient role + + + + + + + + + + + + 1 + + + + A healthcare organization identifier that denotes a physician service. + healthcare physician service identifier + + + + + + + + + + + + + + + An identifier that denotes a healthcare organization service delivery. + An identifier that denotes a healthcare organization service delivery. + + healthcare organization service delivery identifier + + + + + + + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + healthcare organization service delivery beginning temporal information + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + healthcare organization service delivery ending temporal information + + + + + + + + + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + pathological condition impact type on clinical visit + + + + + + + + + + + + + + + + + + + + human clinical visit specified patient + + + + + + + + + + + + + + 1 + + + + + + An identifier that denotes a healthcare provider. + + + healthcare provider identifier + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + 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 + + + + + + + + + identifier + 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. + Justin Whorton + Mathias Brochhausen + proper name + https://github.com/information-artifact-ontology/IAO/issues/237 + Mathias Brochhausen + Sep 29, 2016: The current definition has been amended from the previous version: "A proper name 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." to more accuratly reflect the necessary and sufficient condition on the class. (MB) + identifier + + + + + + + + + + + + + + + + + + + + + Connor, John, born on 28/2/1985 + +Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + + human birth statement + + + + + + + + + + + + + + + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + human birth temporal information + + + + + + + + + An information content entity that denotes the biological sex of an organism. + An information content entity that denotes the biological sex of an organism. + biological sex information content entity + + + + + + + + + A biological sex information content entity that denotes the biological sex of a human. + A biological sex information content entity that denotes the biological sex of a human. + + human biological sex information content entity + + + + + + + + + + + + + + 1 + + + + + + 'Goose' (the name of a cat) + An identifier that denotes a particular organism. + An identifier that denotes a particular organism. + + organism identifier + + + + + + + + + + + + + + 1 + + + + + + An organism identifier that denotes a particular human. + An organism identifier that denotes a particular human. + + + human identifier + + + + + + + + + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + human birth date + + + + + + + + + An information content entity that aims at representing a type of living environment applicable to a primary residence. + living environment type + + + + + + + + + + + + 1 + + + + + Human birth date with data property + MPHPO human birth date + + + + + + + + + + + + 1 + + + + + human biological sex ICE with data property + MPHPO human biological sex information content entity + + + + + + + + + + + + 1 + + + + + ICU admission specification with data property + MPHPO ICU admission specification + + + + + + + + + + + + 1 + + + + + hospitalization admission urgency level specification with data property + MPHPO hospitalization admission urgency level specification + + + + + + + + + + + + 1 + + + + + healthcare physician service identifier with data property + MPHPO healthcare physician service identifier + + + + + + + + + + + + 1 + + + + + pathological condition impact type on clinical visit with data property + MPHPO pathological condition impact type on clinical visit + + + + + + + + + + + + 1 + + + + + pathological condition sub-group name with data property + MPHPO pathological condition sub-group name + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery beginning temporal information with data property + MPHPO healthcare organization service delivery beginning temporal information + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery ending temporal information with data property + MPHPO healthcare organization service delivery ending temporal information + + + + + + + + + + + + 1 + + + + + living environment type with data property + MPHPO living environment type + + + + + + + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota + + + + + + + + + Homo sapiens + human + human being + + + + Homo sapiens + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + + planned process + + + + + + + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + A material entity that is a human made strcuture with firm connection between its foundation and the ground. + Mathias Brochhausen + http://de.wikipedia.org/wiki/Bauwerk + "Building" is a subclass of this. + This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". + architectural structure + + + + + + + + + + + + + + + + + + + + + + + + + + + An architectural structure that bears some function. + Mathias Brochhausen + facility + + + + + + + + + + 09/09/2017 + + + + + + + + + + + + + + + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + It is an open question whether the mereological sum of a request with any other ICE is also a request + request + + + + + It is an open question whether the mereological sum of a request with any other ICE is also a request + hence the definitional necessary condition. + + + + + + + + + + + + + + + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + An information content entity that is the output of a service agreement negociation. + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + service agreement specification + + + + + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + service offer + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + It is an open question whether offering to cook for one's spouse is a service offer. + A service is usually offered for a compensation + + + + + + + + + + + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + temporally qualifying statement + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + More formally, this amount to states that a temporal region overlaps (in the sense of Allen's temporal relations) with a temporal region during which some entity exists. + + + + + + + + + + + + + + + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + process temporally qualifying statement + + + + + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process temporally qualifying statement qualifying temporally the beginning of a process. + process beginning statement + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process that is a mereological sum of temporally disconnected processes has only one process beginning. + + + + + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process temporally qualifying statement qualifying temporally the ending of a process. + process ending statement + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process that is a mereological sum of temporally disconnected processes has only one process ending. + + + + + + + + + + + + + + + + + + + + + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + service agreement negotiation + + + + + + + + + + + + + + + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + service delivery + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + All service deliveries are directed by a service agreement specification, even if this specification is concretized only mentally. + + + + + + + + + An entity that is a disorder, a disease or a pathological bodily process + An entity that is a disorder, a disease or a pathological bodily process + pathological condition + + + + + + + + + + + + + + 1 + + + + + + An information content entity that denotes a one-dimension temporal region. + An information content entity that denotes a one-dimension temporal region. + + temporal information + + + + + + + + + The following is derived from https://en.wikipedia.org/wiki/Statement_(logic): + +Examples of sentences that are (or make) statements: +"Socrates is a man." +"A triangle has three sides." +"Madrid is the capital of Spain." +"There are five ducks on the lake" +"The BRAF V600E mutation causes breast cancer" + +Examples of sentences that are not (or do not make) statements: +"Who are you?" +"Run!" +"Greenness perambulates." +"I had one grunch but the eggplant over there." +"The King of France is wise." +"Broccoli tastes good." + +The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste. + An information content entity expressing a declarative sentence that is either true or false. + From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21): +"A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities." +---- +Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO? + Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made. + +The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth. + statement + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/MPHPO-slim.tsv b/src/ontology/subsets/MPHPO-slim.tsv new file mode 100644 index 0000000..644bb25 --- /dev/null +++ b/src/ontology/subsets/MPHPO-slim.tsv @@ -0,0 +1,105 @@ +?x ?label +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid104 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid118 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid126 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid136 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid140 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid149 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid153 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid167 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid185 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid190 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid93 + "entity" + "continuant" + "occurrent" + "independent continuant" + "temporal region" + "process" + "disposition" + "realizable entity" + "specifically dependent continuant" + "role" + "generically dependent continuant" + "function" + "material entity" + "health procedure" + "health activity" + "health provider identifier" + "health provider role" + "health provider" + "pathological condition sub-group name" + "health procedure specification" + "healthcare service organism specification" + "healthcare facility" + "healthcare organization role" + "healthcare organization" + "healthcare provider" + "healthcare procedure" + "healthcare organization service delivery" + "healthcare organization clinical visit" + "custodial care service delivery" + "healthcare organization identifier" + "inpatient visit" + "hospitalization" + "emergency department visit" + "ambulance initiated emergency department visit" + "healthcare organization service delivery beginning statement" + "healthcare organization service delivery ending statement" + "ambulance paramedics visit" + "ED by ambulance initiated hospitalization" + "ICU admission specification" + "clinical visit agreement specification" + "clinical visit urgency level specification" + "hospitalization admission urgency level specification" + "clinical visit unit type specification" + "healthcare physician service" + "patient" + "patient role" + "healthcare physician service identifier" + "healthcare organization service delivery identifier" + "healthcare organization service delivery beginning temporal information" + "healthcare organization service delivery ending temporal information" + "pathological condition impact type on clinical visit" + "human clinical visit specified patient" + "healthcare provider identifier" + "information content entity" + "directive information entity" + "identifier" + "human birth statement" + "human birth temporal information" + "biological sex information content entity" + "human biological sex information content entity" + "organism identifier" + "human identifier" + "human birth date" + "living environment type" + "MPHPO human birth date" + "MPHPO human biological sex information content entity" + "MPHPO ICU admission specification" + "MPHPO hospitalization admission urgency level specification" + "MPHPO healthcare physician service identifier" + "MPHPO pathological condition impact type on clinical visit" + "MPHPO pathological condition sub-group name" + "MPHPO healthcare organization service delivery beginning temporal information" + "MPHPO healthcare organization service delivery ending temporal information" + "MPHPO living environment type" + "Eukaryota" + "Homo sapiens" + "planned process" + "organization" + "organism" + "architectural structure" + "facility" + "request" + "service agreement specification" + "service offer" + "temporally qualifying statement" + "process temporally qualifying statement" + "process beginning statement" + "process ending statement" + "service agreement negotiation" + "service delivery" + "pathological condition" + "temporal information" + "statement" diff --git a/src/ontology/subsets/RIDDLE_slim.owl b/src/ontology/subsets/RIDDLE_slim.owl deleted file mode 100644 index fc6f373..0000000 --- a/src/ontology/subsets/RIDDLE_slim.owl +++ /dev/null @@ -1,1608 +0,0 @@ - - - - - 2023-10-12 - - - - - - - - - - - - - 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 - - - - - - - - - example of usage - - - - - - - - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - curator note - - - - - - - - - - - - - - - imported from - - - - - - - - - elucidation - - - - - - - - - has associated axiom(nl) - - - - - - - - - has associated axiom(fol) - - - - - - - - - has axiom label - - - - - - - - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - definitional necessary conditions - - - - - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - If we know several definitional necessary conditions associated with an entity, we write as definitional necessary condition the conjunction of them. - - - - - - - - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - definitional necessary and sufficient conditions - - - - - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - If we know several definitional necessary and sufficient conditions associated with an entity, we regroup them in the same annotation. - - - - - - - - Human-readable necessary membership condition(s) of a class or a property. - We introduce 'necessary conditions' rather than 'necessary condition' to avoid the multiplication of annotations. - necessary conditions - - - - - - - - Human-readable necessary and sufficient membership conditions of a class or a property. - necessary and sufficient conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HEPRO-H - - - - - - - - - HOSO classes relevant to humans. - HOSO-H - - - - - - - - - - - - - - - - - IOIO classes relevent to humans. - IOIO-H - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - description - - - - - - - - license - - - - - - - - - - - - - - title - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - 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 - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - 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 - - - - - - - - - TBD - has participating performer - - - - - - - - - TBD - has participating recipient - - - - - - - - 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 - - - - - - - - Inverse of the relation 'mentions' - - - 2022-01-28T07:20:08Z - mentioned by - - - - - - - - - - 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 - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_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 - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - 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. - Alan Ruttenberg - PERSON:Bjoern Peters - is_specified_input_of - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_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 - - - - - - - - - is administered by - - - - - - - - - - - A relation that holds between a filler and a slot it fills. - fills - - - - - - - - - The inverse relations of directs - The inverse relations of directs - is directed by - - - - - - - - - A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. - A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. - is about an aspect of - - - - - - - - A directs B := A is a directive information entity that guides an agent in the execution of B. - A directs B := A is a directive information entity that guides an agent in the execution of B. - directs - - - - - A directs B := A is a directive information entity that guides an agent in the execution of B. - This includes failed attempts where B is not compliant to A. - - - - - - - - - - The inverse relation of fills - The inverse relation of fills - is filled by - - - - - - - - - A maximally directs B := A directs B, and B is compliant to A. - A maximally directs B := A directs B, and B is compliant to A. - Discussed in: Adrien Barton, Laure Vieu, Jean-François Ethier. Directing Actions. Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), Sep 2019, Graz, Austria. - maximally directs - - - - - - - - - The inverse relation of maximally directs. - The inverse relation of maximally directs. - is maximally directed by - - - - - - - - - - The inverse relation of has component. - The inverse relation of has component. - component of - - - - - - - - - - The inverse relation of has component process. - The inverse relation of has component process. - component process of - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - 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 - - has characteristic - - - - - - - - - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - - - - - - - - - inverse of has disposition - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - has component process - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - - David Osumi-Sutherland - d - during - - - - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by - - starts with - - - - - - - - - - - - inverse of ends with - - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes - - - - - has input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces - - - - - has output - - - - - - - - - - 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 - - - - - - - - - inverse of has input - - - - input of - - - - - - - - - inverse of has output - - - - output of - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - - - has part that occurs in - - - - - - - - - - x agent_in y iff y is an instance of Process and x is an instance of Agent, such that x is causally active in y. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - agent in - - - - - - - - - x has_agent y iff x is an instance of Process and y is an instance of Agent, such that y is causally active in x. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - has agent - - - - - - - - - x has_capability y iff x is an instance of Agent and y is an instance of Agent Capability, such that x bearer of y. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - has capability - - - - - - - diff --git a/src/ontology/subsets/RIDDLE_slim.tsv b/src/ontology/subsets/RIDDLE_slim.tsv deleted file mode 100644 index e69de29..0000000 diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100644 index 0000000..45d431d --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 31d658f..3d27b10 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -26,7 +26,8 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ mkdir -p $ROOTDIR/.github mkdir -p $ROOTDIR/.github/workflows -cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml +cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml @@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml cp -n target/$OID/mkdocs.yaml $ROOTDIR/ echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" -echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." + echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 0000000..a6a4851 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix \ No newline at end of file diff --git a/src/sparql/dc-properties-violation.sparql b/src/sparql/dc-properties-violation.sparql new file mode 100644 index 0000000..b04e819 --- /dev/null +++ b/src/sparql/dc-properties-violation.sparql @@ -0,0 +1,11 @@ +# The purpose of this violation is to make sure people update +# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/) +# to using the recommended DC Terms namespace (http://purl.org/dc/terms/) +# See also discussion on https://github.com/oborel/obo-relations/pull/692 + +SELECT ?term ?predicate WHERE { + ?term ?predicate ?value . + FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RIDDLE_"))) +} + diff --git a/subsets/MPHPO-Slim.owl b/subsets/MPHPO-Slim.owl new file mode 100644 index 0000000..9a906e0 --- /dev/null +++ b/subsets/MPHPO-Slim.owl @@ -0,0 +1,4065 @@ + + + + + 2024-08-02 + + + + + + + + + + + + + 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 + + + + + + + + + example of usage + + + + + + + + + + + + + + + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + curator note + + + + + + + + + + + + + + + imported from + + + + + + + + + elucidation + + + + + + + + + has associated axiom(nl) + + + + + + + + + has associated axiom(fol) + + + + + + + + + has axiom label + + + + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary conditions + + + + + Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary conditions associated with an entity, we write as definitional necessary condition the conjunction of them. + + + + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + definitional necessary and sufficient conditions + + + + + A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. + If we know several definitional necessary and sufficient conditions associated with an entity, we regroup them in the same annotation. + + + + + + + + Human-readable necessary membership condition(s) of a class or a property. + We introduce 'necessary conditions' rather than 'necessary condition' to avoid the multiplication of annotations. + necessary conditions + + + + + + + + Human-readable necessary and sufficient membership conditions of a class or a property. + necessary and sufficient conditions + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subset for RIDDLE project + MPHPO-Slim + + + + + + + + + OpenLHS classes relevant to humans. + OpenLHS-H + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ISO8601 DateTime + + + + + + + + + + + + + + + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 + + + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + TBD + has participating performer + + + + + + + + + TBD + has participating recipient + + + + + + + + + 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 + + + + + + + + Inverse of the relation 'mentions' + + + 2022-01-28T07:20:08Z + mentioned by + + + + + + + + + + + + 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 + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + The inverse property of is_specified_input_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 + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + 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. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + The inverse property of is_specified_output_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 + + + + + + + + + is administered by + + + + + + + + + + + A relation that holds between a filler and a slot it fills. + fills + + + + + + + + + + + The inverse relations of directs + The inverse relations of directs + is directed by + + + + + + + + + + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. + is about an aspect of + + + + + + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + A directs B := A is a directive information entity that guides an agent in the execution of B. + directs + + + + + A directs B := A is a directive information entity that guides an agent in the execution of B. + This includes failed attempts where B is not compliant to A. + + + + + + + + + + The inverse relation of fills + The inverse relation of fills + is filled by + + + + + + + + + + + A maximally directs B := A directs B, and B is compliant to A. + A maximally directs B := A directs B, and B is compliant to A. + Discussed in: Adrien Barton, Laure Vieu, Jean-François Ethier. Directing Actions. Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), Sep 2019, Graz, Austria. + maximally directs + + + + + + + + + + + The inverse relation of maximally directs. + The inverse relation of maximally directs. + is maximally directed by + + + + + + + + + + The inverse relation of has component. + The inverse relation of has component. + component of + + + + + + + + + + + + The inverse relation of has component process. + The inverse relation of has component process. + component process of + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic + + + + + + + + + + + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + 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 + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + + 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 + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + + x agent_in y iff y is an instance of Process and x is an instance of Agent, such that x is causally active in y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + agent in + + + + + + + + + x has_agent y iff x is an instance of Process and y is an instance of Agent, such that y is causally active in x. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has agent + + + + + + + + + x has_capability y iff x is an instance of Agent and y is an instance of Agent Capability, such that x bearer of y. + http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology + has capability + + + + + + + + + + + + + + has textual representation + + + + + + + + + has value + + + + + + + + + has numerical value + + + + + + + + + has temporal value + + + + + + + + + has text value + + + + + + + + + + + + + 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 + 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 + 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 + 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] + + + + + + + + + + + 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] + + + + + + + + + + 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. + 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 + + + + + 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 + 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] + + + + + + + + + + + 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 + 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 + 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. + 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 + + + + + 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] + + + + + + + + + + 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. + 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] + + + + + + + + + + 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 + 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 + + + + + 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] + + + + + + + + + + + + + + + + + + + + + + + + + + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + A planned process that has some components that are planned processes, including at least one that is a health activity. + - A planned process that is maximally directed by a health procedure specification. +- A planned process that is guided by the objective of contributing to a desired effect on the health status of an organism or several organisms achieved through the treatment, diagnosis, or prevention of disease or injury. + + + health procedure + + + + + + + + + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + A planned process that aims to produce a truthful statement about the health status of an organism or modify it. + + health activity + + + + + + + + + + + + 1 + + + + An individual identifier that denotes a health provider. + + + health provider identifier + + + + + + + + + + + + + + + A role that inheres in an organism as a consequence of training in order to be able to participate as a performer in some health activities. + This usually includes health professional like physicians, nurses or pharmacists etc. +It could also includes non professionals like patient attendant but it would exclude others like secretaries or accountants. + + health provider role + + + + + + + + + + + + + + + An organism that is the bearer of a health provider role. + + + health provider + + + + + + + + + + + + + + + An information content entity that is about a sub-group of pathological conditions. + We suppose that if an ICE is about a group of particular entities, it is also about each of these entities. + pathological condition sub-group name + + + + + + + + + A directive information entity that aims to direct a health procedure. + A directive information entity that aims to direct a health procedure. + + health procedure specification + + + + + + + + + + + + + + + A service agreement specification identifying an organism for whom a healthcare service delivery aims at providing a desired effect to its health status. + + healthcare service organism specification + + + + + + + + + A facility that bears a healthcare function - WiP. + healthcare facility + + + + + + + + + A role that inheres in an organisation and is realized by providing some healthcare service delivery. + healthcare organization role + + + + + + + + + + + + + + + An organisation that bears a healthcare organisation role. + healthcare organization + + + + + + + + + + + + + + + + + + + A health provider who is a member of a healthcare organisation. + + healthcare provider + + + + + + + + + + + + + + + A health procedure that is part of a healthcare service delivery and that is performed by a healthcare worker while realizing its health care worker role. + healthcare procedure + + + + + + + + + + + + + + + A service delivery under the responsibility of a healthcare organisation. It stems from an agreement between a requesting agent and a healthcare organization. + + + healthcare organization service delivery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + A healthcare organisation service delivery that aims at providing a desired effect on the health status of a specified organism. It is usually composed of health procedures and possibly associated ancillary processes. + + + healthcare organization clinical visit + + + + + + + + + A service delivery from an organization that aims to provide for the activities of daily living of individuals or communities. + + custodial care service delivery + + + + + + + + + + + + 1 + + + + An identifier that denotes a healthcare organization. + healthcare organization identifier + + + + + + + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing support for activities of daily living (such as eating and bathing) and accommodation for the patient. + + inpatient visit + + + + + + + + + An inpatient visit located in a hospital facility requested by a physician, that may extends overnight. + + + hospitalization + + + + + + + + + + + + + + + A healthcare organisation clinical visit where there is expectation of providing unplanned, timely, urgent care, including handling life-threatening conditions. +It is not necessarily an immediate inpatient subsequent visit. + + + emergency department visit + + + + + + + + + + + + + + + + + + + An emergency department visit for a given patient that was participating in another healthcare organisation visit involving paramedics just prior to this visit. + Considérer axomatisation séquentielle + + + ambulance initiated emergency department visit + + + + + + + + + + + + + + + + + + + + + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + A process beginning statement that temporally qualifies the beginning of a healthcare organisation service delivery. + + + healthcare organization service delivery beginning statement + + + + + + + + + + + + + + + + + + + + + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + A process ending statement that temporally qualifies the ending of a healthcare organisation service delivery. + + + healthcare organization service delivery ending statement + + + + + + + + + A healthcare organization clinical visit involving an ambulance and paramedics as healthcare provider. + + ambulance paramedics visit + + + + + + + + + + + + + + + + + + + + An hospitalization for a given patient that was participating in an ambulance initiated emergency departement visit. + + ED by ambulance initiated hospitalization + + + + + + + + + A clinical visit unit type specification mandating an hospitalization admission to an intensive care unit. + ICU admission specification + + + + + + + + + A service agreement specification for a clinical visit admission. + clinical visit agreement specification + + + + + + + + + A clinical visit agreement specification mandating the urgency level of the clinical visit. + clinical visit urgency level specification + + + + + + + + + A clinical visit urgency level specification mandating the urgency level of the hospitalization admission. + hospitalization admission urgency level specification + + + + + + + + + A clinical visit agreement specification mandating the type of unit required for a clinical visit. + clinical visit unit type specification + + + + + + + + + + + + + + + A healthcare organization with a mandate to manage and coordinate healthcare procedures deliveries under the responsability of its members + It is often a sub-organization of a department. Ex: General internal medicine service is under the medicine department. + It is often based on the specialty of its members (e.g. respirology), but not always (e.g. vascular service, which may include general internal medicine physician as well as vascular surgeon). + healthcare physician service + + + + + + + + + + + + + + + An eukaryote that is the bearer of a patient role. + patient + + + + + + + + + + + + + + + A role born by an organism which is the primary recipient in a healthcare organization clinical visit. + patient role + + + + + + + + + + + + 1 + + + + A healthcare organization identifier that denotes a physician service. + healthcare physician service identifier + + + + + + + + + + + + + + + An identifier that denotes a healthcare organization service delivery. + An identifier that denotes a healthcare organization service delivery. + + healthcare organization service delivery identifier + + + + + + + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery beginning statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the beginning of healthcare organization service delivery. + healthcare organization service delivery beginning temporal information + + + + + + + + + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + A temporal information that is a component of a healthcare organization service delivery ending statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the ending of healthcare organization service delivery. + healthcare organization service delivery ending temporal information + + + + + + + + + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + An information content entity that describes the type of impact of a pathological condition on a clinical visit. + pathological condition impact type on clinical visit + + + + + + + + + + + + + + + + + + + + human clinical visit specified patient + + + + + + + + + + + + + + 1 + + + + + + An identifier that denotes a healthcare provider. + + + healthcare provider identifier + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + 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 + + + + + + + + + identifier + 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. + Justin Whorton + Mathias Brochhausen + proper name + https://github.com/information-artifact-ontology/IAO/issues/237 + Mathias Brochhausen + Sep 29, 2016: The current definition has been amended from the previous version: "A proper name 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." to more accuratly reflect the necessary and sufficient condition on the class. (MB) + identifier + + + + + + + + + + + + + + + + + + + + + Connor, John, born on 28/2/1985 + +Connor, John, born on 28/2/1985, son of Connor, Sarah born on 13/11/1965 + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + A process temporally qualifying statement about the birth of a human including an identifier and a temporal information of the birth of this human. + + human birth statement + + + + + + + + + + + + + + + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + A temporal information that is a component of a human birth statement that states that the temporal region denoted by this temporal information overlaps with the temporal region occupied by the birth of this human. + human birth temporal information + + + + + + + + + An information content entity that denotes the biological sex of an organism. + An information content entity that denotes the biological sex of an organism. + biological sex information content entity + + + + + + + + + A biological sex information content entity that denotes the biological sex of a human. + A biological sex information content entity that denotes the biological sex of a human. + + human biological sex information content entity + + + + + + + + + + + + + + 1 + + + + + + 'Goose' (the name of a cat) + An identifier that denotes a particular organism. + An identifier that denotes a particular organism. + + organism identifier + + + + + + + + + + + + + + 1 + + + + + + An organism identifier that denotes a particular human. + An organism identifier that denotes a particular human. + + + human identifier + + + + + + + + + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + A human birth temporal information that denotes a time interval of one day as defined in a calendar accepted in a human society. + human birth date + + + + + + + + + An information content entity that aims at representing a type of living environment applicable to a primary residence. + living environment type + + + + + + + + + + + + 1 + + + + + Human birth date with data property + MPHPO human birth date + + + + + + + + + + + + 1 + + + + + human biological sex ICE with data property + MPHPO human biological sex information content entity + + + + + + + + + + + + 1 + + + + + ICU admission specification with data property + MPHPO ICU admission specification + + + + + + + + + + + + 1 + + + + + hospitalization admission urgency level specification with data property + MPHPO hospitalization admission urgency level specification + + + + + + + + + + + + 1 + + + + + healthcare physician service identifier with data property + MPHPO healthcare physician service identifier + + + + + + + + + + + + 1 + + + + + pathological condition impact type on clinical visit with data property + MPHPO pathological condition impact type on clinical visit + + + + + + + + + + + + 1 + + + + + pathological condition sub-group name with data property + MPHPO pathological condition sub-group name + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery beginning temporal information with data property + MPHPO healthcare organization service delivery beginning temporal information + + + + + + + + + + + + 1 + + + + + healthcare organization service delivery ending temporal information with data property + MPHPO healthcare organization service delivery ending temporal information + + + + + + + + + + + + 1 + + + + + living environment type with data property + MPHPO living environment type + + + + + + + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota + + + + + + + + + Homo sapiens + human + human being + + + + Homo sapiens + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + + planned process + + + + + + + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + A material entity that is a human made strcuture with firm connection between its foundation and the ground. + Mathias Brochhausen + http://de.wikipedia.org/wiki/Bauwerk + "Building" is a subclass of this. + This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". + architectural structure + + + + + + + + + + + + + + + + + + + + + + + + + + + An architectural structure that bears some function. + Mathias Brochhausen + facility + + + + + + + + + + 09/09/2017 + + + + + + + + + + + + + + + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + An information content entity specifiying one or several types of processes that a party, whether a person or an organization, wants to see instantiated for the benefit of itself or another party. + It is an open question whether the mereological sum of a request with any other ICE is also a request + request + + + + + It is an open question whether the mereological sum of a request with any other ICE is also a request + hence the definitional necessary condition. + + + + + + + + + + + + + + + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + An information content entity that is the output of a service agreement negociation. + An information content entity that specifies a service agreement made between a request party and a service offer party, and aim to direct some processes that correspond to what has been agreed between the parties. + service agreement specification + + + + + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + service offer + + + + + An information content entity describing the processes a person or an organization is willing to perform for a third-party. + It is an open question whether offering to cook for one's spouse is a service offer. + A service is usually offered for a compensation + + + + + + + + + + + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + temporally qualifying statement + + + + + A statement that states that an entity existed, exists or will exist at some point during a specified temporal region. + More formally, this amount to states that a temporal region overlaps (in the sense of Allen's temporal relations) with a temporal region during which some entity exists. + + + + + + + + + + + + + + + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + A temporally qualifying statement stating that a temporal region overlaps with a temporal region during which some process occurred, occurs or will occur. + process temporally qualifying statement + + + + + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process temporally qualifying statement qualifying temporally the beginning of a process. + process beginning statement + + + + + A process temporally qualifying statement qualifying temporally the beginning of a process. + A process that is a mereological sum of temporally disconnected processes has only one process beginning. + + + + + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process temporally qualifying statement qualifying temporally the ending of a process. + process ending statement + + + + + A process temporally qualifying statement qualifying temporally the ending of a process. + A process that is a mereological sum of temporally disconnected processes has only one process ending. + + + + + + + + + + + + + + + + + + + + + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + A planned process of interaction between a request party and a service offer party having as specified input some request and some service offer and that aims to generate as output a service agreement. + service agreement negotiation + + + + + + + + + + + + + + + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + service delivery + + + + + - A planned process that aims at fulfilling the commitments of a service agreement. + +- A planned process that is maximally directed by a service agreement specification. + All service deliveries are directed by a service agreement specification, even if this specification is concretized only mentally. + + + + + + + + + An entity that is a disorder, a disease or a pathological bodily process + An entity that is a disorder, a disease or a pathological bodily process + pathological condition + + + + + + + + + + + + + + 1 + + + + + + An information content entity that denotes a one-dimension temporal region. + An information content entity that denotes a one-dimension temporal region. + + temporal information + + + + + + + + + The following is derived from https://en.wikipedia.org/wiki/Statement_(logic): + +Examples of sentences that are (or make) statements: +"Socrates is a man." +"A triangle has three sides." +"Madrid is the capital of Spain." +"There are five ducks on the lake" +"The BRAF V600E mutation causes breast cancer" + +Examples of sentences that are not (or do not make) statements: +"Who are you?" +"Run!" +"Greenness perambulates." +"I had one grunch but the eggplant over there." +"The King of France is wise." +"Broccoli tastes good." + +The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste. + An information content entity expressing a declarative sentence that is either true or false. + From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21): +"A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities." +---- +Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO? + Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made. + +The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth. + statement + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/MPHPO-Slim.tsv b/subsets/MPHPO-Slim.tsv new file mode 100644 index 0000000..644bb25 --- /dev/null +++ b/subsets/MPHPO-Slim.tsv @@ -0,0 +1,105 @@ +?x ?label +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid104 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid118 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid126 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid136 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid140 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid149 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid153 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid167 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid185 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid190 +_:B4123111eX2D32e0X2D4a9dX2Dbfa6X2D88367906d58egenid93 + "entity" + "continuant" + "occurrent" + "independent continuant" + "temporal region" + "process" + "disposition" + "realizable entity" + "specifically dependent continuant" + "role" + "generically dependent continuant" + "function" + "material entity" + "health procedure" + "health activity" + "health provider identifier" + "health provider role" + "health provider" + "pathological condition sub-group name" + "health procedure specification" + "healthcare service organism specification" + "healthcare facility" + "healthcare organization role" + "healthcare organization" + "healthcare provider" + "healthcare procedure" + "healthcare organization service delivery" + "healthcare organization clinical visit" + "custodial care service delivery" + "healthcare organization identifier" + "inpatient visit" + "hospitalization" + "emergency department visit" + "ambulance initiated emergency department visit" + "healthcare organization service delivery beginning statement" + "healthcare organization service delivery ending statement" + "ambulance paramedics visit" + "ED by ambulance initiated hospitalization" + "ICU admission specification" + "clinical visit agreement specification" + "clinical visit urgency level specification" + "hospitalization admission urgency level specification" + "clinical visit unit type specification" + "healthcare physician service" + "patient" + "patient role" + "healthcare physician service identifier" + "healthcare organization service delivery identifier" + "healthcare organization service delivery beginning temporal information" + "healthcare organization service delivery ending temporal information" + "pathological condition impact type on clinical visit" + "human clinical visit specified patient" + "healthcare provider identifier" + "information content entity" + "directive information entity" + "identifier" + "human birth statement" + "human birth temporal information" + "biological sex information content entity" + "human biological sex information content entity" + "organism identifier" + "human identifier" + "human birth date" + "living environment type" + "MPHPO human birth date" + "MPHPO human biological sex information content entity" + "MPHPO ICU admission specification" + "MPHPO hospitalization admission urgency level specification" + "MPHPO healthcare physician service identifier" + "MPHPO pathological condition impact type on clinical visit" + "MPHPO pathological condition sub-group name" + "MPHPO healthcare organization service delivery beginning temporal information" + "MPHPO healthcare organization service delivery ending temporal information" + "MPHPO living environment type" + "Eukaryota" + "Homo sapiens" + "planned process" + "organization" + "organism" + "architectural structure" + "facility" + "request" + "service agreement specification" + "service offer" + "temporally qualifying statement" + "process temporally qualifying statement" + "process beginning statement" + "process ending statement" + "service agreement negotiation" + "service delivery" + "pathological condition" + "temporal information" + "statement" diff --git a/subsets/RIDDLE_slim.owl b/subsets/RIDDLE_slim.owl deleted file mode 100644 index fc6f373..0000000 --- a/subsets/RIDDLE_slim.owl +++ /dev/null @@ -1,1608 +0,0 @@ - - - - - 2023-10-12 - - - - - - - - - - - - - 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 - - - - - - - - - example of usage - - - - - - - - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - curator note - - - - - - - - - - - - - - - imported from - - - - - - - - - elucidation - - - - - - - - - has associated axiom(nl) - - - - - - - - - has associated axiom(fol) - - - - - - - - - has axiom label - - - - - - - - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - definitional necessary conditions - - - - - Necessary condition that is definitional, that is the notion to be defined does not appear in the condition. - If we know several definitional necessary conditions associated with an entity, we write as definitional necessary condition the conjunction of them. - - - - - - - - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - definitional necessary and sufficient conditions - - - - - A necessary and sufficient condition that is definitional, that is the notion to be defined does not appear in the condition. - If we know several definitional necessary and sufficient conditions associated with an entity, we regroup them in the same annotation. - - - - - - - - Human-readable necessary membership condition(s) of a class or a property. - We introduce 'necessary conditions' rather than 'necessary condition' to avoid the multiplication of annotations. - necessary conditions - - - - - - - - Human-readable necessary and sufficient membership conditions of a class or a property. - necessary and sufficient conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HEPRO-H - - - - - - - - - HOSO classes relevant to humans. - HOSO-H - - - - - - - - - - - - - - - - - IOIO classes relevent to humans. - IOIO-H - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - description - - - - - - - - license - - - - - - - - - - - - - - title - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - 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 - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - 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 - - - - - - - - - TBD - has participating performer - - - - - - - - - TBD - has participating recipient - - - - - - - - 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 - - - - - - - - Inverse of the relation 'mentions' - - - 2022-01-28T07:20:08Z - mentioned by - - - - - - - - - - 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 - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_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 - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - 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. - Alan Ruttenberg - PERSON:Bjoern Peters - is_specified_input_of - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_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 - - - - - - - - - is administered by - - - - - - - - - - - A relation that holds between a filler and a slot it fills. - fills - - - - - - - - - The inverse relations of directs - The inverse relations of directs - is directed by - - - - - - - - - A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. - A is about an aspect of B := A is about a specifically dependent continuant that inheres in B. - is about an aspect of - - - - - - - - A directs B := A is a directive information entity that guides an agent in the execution of B. - A directs B := A is a directive information entity that guides an agent in the execution of B. - directs - - - - - A directs B := A is a directive information entity that guides an agent in the execution of B. - This includes failed attempts where B is not compliant to A. - - - - - - - - - - The inverse relation of fills - The inverse relation of fills - is filled by - - - - - - - - - A maximally directs B := A directs B, and B is compliant to A. - A maximally directs B := A directs B, and B is compliant to A. - Discussed in: Adrien Barton, Laure Vieu, Jean-François Ethier. Directing Actions. Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), Sep 2019, Graz, Austria. - maximally directs - - - - - - - - - The inverse relation of maximally directs. - The inverse relation of maximally directs. - is maximally directed by - - - - - - - - - - The inverse relation of has component. - The inverse relation of has component. - component of - - - - - - - - - - The inverse relation of has component process. - The inverse relation of has component process. - component process of - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - 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 - - has characteristic - - - - - - - - - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - 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 - - - - - - - - - inverse of has disposition - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - has component process - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - - David Osumi-Sutherland - d - during - - - - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by - - starts with - - - - - - - - - - - - inverse of ends with - - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes - - - - - has input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces - - - - - has output - - - - - - - - - - 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 - - - - - - - - - inverse of has input - - - - input of - - - - - - - - - inverse of has output - - - - output of - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - - - has part that occurs in - - - - - - - - - - x agent_in y iff y is an instance of Process and x is an instance of Agent, such that x is causally active in y. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - agent in - - - - - - - - - x has_agent y iff x is an instance of Process and y is an instance of Agent, such that y is causally active in x. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - has agent - - - - - - - - - x has_capability y iff x is an instance of Agent and y is an instance of Agent Capability, such that x bearer of y. - http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology - has capability - - - - - - - diff --git a/subsets/RIDDLE_slim.tsv b/subsets/RIDDLE_slim.tsv deleted file mode 100644 index e69de29..0000000