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@brynnz22 brynnz22 released this 29 Nov 20:46
· 359 commits to main since this release
v2.0.0
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Learn about vigilant mode.

Includes the following changes:

Version Date Author Decision Rationale
2.0.0 8/25/2021 RJA Remove 'list' validation for 'synonyms' Validation not required, as values are not restricted.
2.0.0 8/26/2021 RJA Revert last change List validation is required, but the validation introduces confusing instructions. Issue filed: Sage-Bionetworks/schematic#512
2.0.0 8/31/2021 MD Completely reworked data model Allows for RDB instantiation within schematics framework.
2.0.0 9/7/2021 BZ Change Description attribute to optional Will not have description data for every resource, such as antibodies.
2.0.0 9/7/2021 BZ Delete donor_id from DependsOn and Properties columns of Antibody. Delete Donor from DependsOn Component column for Antibody. Antibody does not need to have a relationship to the donor table.
2.0.0 9/8/2021 BZ Change clone Id to not required Many clone ids are not provided or not relevant to polyclonal antibodies.
2.0.0 9/9/2021 BZ Added: Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish to valid values for Antibody Reactive Species
2.0.0 9/9/2021 BZ Added: Mouse, Rabbit as valid values for Host Organism for Antibody table. Values listed from Scicrunch Data
2.0.0 9/9/2021 MD Added VendorItemId as a depends on item for Resource  
2.0.0 9/9/2021 MD Added MTA Required, Usage Requirements, Date Added, Date Modified to the depends on and properties for Resource.  
2.0.0 9/10/2021 BZ Add resource_id as a dependsOn and Property value for Vendor Item. Add Resource as a DependsOn Component for Vendor Item. Remove vendor_item_id as a DependsOn and Property value for Resource. Remove Vendor Item as a DependsOn Component for Resource. Switch dependency of Resource Table with Vendor Item table to account for multiple vendor items per resource.
2.0.0 9/10/2021 BZ Set Catalog Number requirement of Vendor Item table to TRUE Should be required if vendor Item table is filled out.
2.0.0 9/21/2021 RJA Changed "Sex" to not required Animal models are often available in both sexes, not just one, so is not really relevant to this resource type.
2.0.0 9/21/2021 RJA Added "gene trapped" mutation method Term needed for curation.
2.0.0 9/27/2021 RJA added "external mutation ID' attribute To allow references to MGI or other external well-curated variant databases
2.0.0 9/27/2021 RJA Added "unknown" value to "usage requirements" Term needed for curation.
2.0.0 9/27/2021 RJA Modifed Mutation Type, Mutation Method to be aligned with MGI phenotypic allele category (http://www.informatics.jax.org/userhelp/ALLELE_phenotypic_categories_help.shtml) vocabulary. This includes most of the terms we currently need and several others that may be useful when opening for community contributions.
2.0.0 9/27/2021 RJA Added "Applications" Attribute to Resource Applications component. Missing attribute.
2.0.0 9/27/2021 RJA Renamed "Genetic Background" to "Background Strain" To improve clarity.
2.0.0 9/27/2021 RJA Added "Background Substrain" attribute. To capture animal model substrains.
2.0.0 9/27/2021 RJA Removed "strain" and "breed" from donor. Redundant with animal model strain, substrain, and model nomenclature attributes.
2.0.0 9/28/2021 RJA Added "Allele Type", and aligned vocabulary with MGI dictionary. This term was a confounded with "Mutation Method" but captures distinct concepts.
2.0.0 9/28/2021 RJA Added "External mutation ID" attribute to Mutation DependsOn. Bugfix, missed previously
2.0.0 9/28/2021 RJA Added "Applications" Attribute to Resource Applications DependsOn. Bugfix, missed previously
2.0.0 9/28/2021 RJA Added Tumor Types "atypical neurofiibroma, neurofibroma NOS, diffuse infiltrating neurofibroma" Terms needed for curation.
2.0.0 9/28/2021 RJA Fixed Specimen Preparation Method typo Bugfix to get terms to populate correctly.
2.0.0 9/28/2021 RJA Fixed Cryopreserved Typo Bugfix.
2.0.0 9/28/2021 RJA Changed Funder_id and Funder Name to not required This information will not always be available.
2.0.0 9/30/2021 BZ Delete Alt Insert Name from Genetic Reagent Table This is redundant to synonyms in the Resource table
2.0.0 9/30/2021 RJA Change "gRNA shRNA sequence" definition Minor changes for clarity.
2.0.0 9/30/2021 BZ Add "Transfer Vector" as valid value for Vector Type in Genetic Reagent Table A vector type for NF1 plasmids.
2.0.0 9/30/2021 BZ Add "Gateway Entry Clone" as valid value for Vector Type in Genetic Reagent Table A vector type for NF1 plasmids.
2.0.0 9/30/2021 BZ Add "DH10B" as Growth Strain for Genetic Reagents Table A growth strain for plasmids.
2.0.0 9/30/2021 BZ Add "Homo sapiens" and "Mus musculus" and "Rattus norvegicus" to insert Species valid values for Genetic Reagents Table Insert species for plasmids.
2.0.0 9/30/2021 BZ Change Insert Size as not required for Genetic Reagent table Not always available
2.0.0 10/1/2021 BZ Add "Depositor Comment" and "Usage Instructions" as valid values for Observation Type These are observation types for plasmids.
2.0.0 10/1/2021 BZ Delete "Observation Submitter Id" and add "ObervationSubmitterName" Not all observation submitters will have a synapse id.
2.0.0 10/1/2021 RJA Set "Applications" Attribute requirement (True) This should be required when providing Resorce Applications data
2.0.0 10/4/2021 BZ Add synapse_Id to Obervation table. List Investigator_id to as DependsOn for Observation. And Investigator as DependsOn Component for Observation. Include necessary identifiers to observation table.
2.0.0 10/4/2021 RJA Add mutation type: "Loss of heterozygosity (unspecified mechanism)" Needed for curation.
2.0.0 10/4/2021 RJA Changed "Animal Mimic Mutation" to "Human ClinVar Mutation" Better described the data being collected for this attribute.
2.0.0 10/4/2021 RJA Removed "Genotype" attribute from mutation component This is no longer applicable with one mutation per row data structure, as it describes 2 alleles, not just one.
2.0.0 10/4/2021 RJA Add usage requirement: "unknown" This information is not always publicly surfaced.
2.0.0 10/5/2021 RJA Change "ObservationSubmitterName" to "Observation Submitter Name" Match naming convention for other attributes.
2.0.0 10/5/2021 RJA Change "Synapse_Id" to "Synapse_id" Match naming convention for other attributes.
2.0.0 10/5/2021 BZ Add "Source" as an attribute of ResourceApplication with valid values of "Community," "Investigator", and "Vendor" To identify who is providing the resource applicaiton information.
2.0.0 10/5/2021 BZ Append "-reported" to the end of each valid value for "Source" To avoid schematic appending Vendor and Investigator tables onto the ResourceApplications table. Need to give unique name to Vendor and Investigator valid values.
2.0.0 10/5/2021 BZ Add "Immunoprecipitation" as a valid value for "Applications" A type of resource applicaiton.
2.0.0 10/5/2021 RJA Add "Publication_id" to Observation component Allows a submitter to link/attribute a published article to an Observation
2.0.0 10/6/2021 BZ Add "Immunohistochemistry (Paraffin-Embedded)" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Immunocytochemistry" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Immunohistochemistry (Frozen Sections)" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Flow Cytometry" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Affinity Purification" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Microarray" as a value for Application A type of resource application.
2.0.0 10/6/2021 BZ Add "Usage" table that DependsOn Component "Publication" and "Resource". Add "Usage_id" for "Usage" table. Create a table to list usage publications separate from development publications.
2.0.0 10/6/2021 BZ Delete Publication_id as a DependsOn and Properties for ResourceApplications. Delete "Publication" as a DependsOn Component for ResourceApplications. Made Usage Publication its own table, so can delete publication info. from ResourceApplications table.
2.0.0 10/7/2021 RJA Added Escherichia coli species Needed for curation of DH5alpha cells.
2.0.0 10/7/2021 RJA Added "special licencing restrictions (see vendor for more information)" to usage restrictions To handle scenarios where there are complex licenses describing usage (e.g. non-commercial use except for when you pay for a specific license to commercialize this product).
2.0.0 10/7/2021 RJA Added 'disease' Cancer To accomodate non-NF related cancers or cell lines from non-NF cancer patients. At a future date, could be deprecated in place of more specific terminology.
2.0.0 10/13/21 RJA Changed "Transplation Type" to "Transplantion Type" Typo in attribute name prevents attribute properties from being applied
2.0.0 10/13/21 MD Remove 'list' validation for 'mutation_id' Will handle mutation_id now in an association table
2.0.0 10/13/21 MD Add Mutation Burden association table Allows many to many relationships with mutation_id
2.0.0 10/13/21 MD Change name for mutation Burden to Mutation, and Mutation table to Mutation Details For clarification of roles the tables play.
2.0.0 10/14/2021 RJA Add "citation" attribute and add to publications component Largetext citation needed to support front end design.
2.0.0 10/14/2021 RJA Enhance 'doi' definition (added "in the form of https://www.doi.org/{doi} to comply with CrossRef display guidelines.) To comply with DOI display guidelines from CrossRef and to avoid need for frontend conversion of doi to link.
2.0.0 10/14/2021 RJA Remove investigator_id from Observations component Redundant with Submitter Name/utility is not clear
2.0.0 10/14/2021 RJA Add "Observation Link" to "Observation" attribute to capture non-published links
2.0.0 11/3/21 MD "Insert Entrez_id" to "Entrez ID"; "Synapse_id" to "Synapse ID" keeping _id reserved for Pks
2.0.0 11/8/21 MD MutationDetailsID as list, change Sequence Variation ; Protein Variation; Animal Model Mutation; Human ClinVar Mutation to not be a list. Data types.
2.0.0 11/15/21 MD Added Publication Date Unix column to allow tracking of these dates Need to allow the portal to access time both as a string and a unix time date.
2.0.0 11/18/21 MD Delete Publication from DependsOnComponent to match earlier removal of publicationId  
2.0.0 11/18/21 MD Add list validation rule to Applications Allow them to be caputred as a list
Assets 2
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