v4.0.0

What's Changed

• Update README.md by @cconrad8 in #27
• Feat/schema viz dev by @brynnz22 in #28
• Remove MTA Required from data model by @allaway in #31
• change disease concept to genetic disorder by @allaway in #30
• Update workflow to py3.10 by @allaway in #33
• Update schematic-schema-convert.yml by @allaway in #35
• attempt to bugfix workflow by @allaway in #37
• Update schematic-schema-convert.yml by @allaway in #42
• Reprocess schema with schematic 23.6.1 by @allaway in #43
• Fix error with donor domainIncludes by @allaway in #44
• fix title capitalization by @allaway in #46
• Add publication component to observation by @allaway in #47
• add publication_id to scope of publication by @allaway in #48
• fix stray column by @allaway in #49
• fix stray column #2 by @allaway in #50
• Update nf_research_tools.rdb.model.csv by @cconrad8 in #53
• Major update by @allaway in #54

New Contributors

• @cconrad8 made their first contribution in #27

Full Changelog: v3.0.0...v4.0.0

v3.0.0

What's Changed

• Update schematic-schema-convert.yml by @allaway in #21
• add venv and roll back to py3.8 by @allaway in #22
• Update nf_research_tools.rdb.model.csv by @allaway in #25

Full Changelog: v2.0.1...v3.0.0

v2.0.1

What's Changed

• Add new badges by @allaway in #5
• Update README.md by @brynnz22 in #6
• Add schematic-schema-convert.yml by @allaway in #7
• add schema csv by @allaway in #12
• Add "How to Acquire" attribute by @allaway in #13
• Missing howToAcquire by @allaway in #16
• simple commit to trigger pr rebuild by @allaway in #17
• revert last change. by @allaway in #18

Full Changelog: v2.0.0...v2.0.1

Schema v2.0.0

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 ass...

Schema v1.0.1

Includes the following changes:

Version	Date	Author	Decision	Rationale
1.0.1	8/24/2021	RJA, BZ	Updated newAnimal, newCellLine, newGeneticReagent, newAntibody template definitions	A second pass on these manifests based on filling in prototype data; newGeneticReagent and newAntibody have no prototype data yet. All manifests subject to change, still.

Note: in this release, the v1.0.1 JSON-LD file was mistakenly named "nfti.jsonld".

Schema v1.0.0

This release contains all initial schema development work to populate the dictionary, as well as the following logged changes:

Date	Author	Decision	Rationale
8/15/2021	RJA	add genetic reagent manifest (newGeneticReagent)	for testing purposes; may be able to be removed later if components are refined, or redefined using components
8/17/2021	BZ	Add "list" as validation rule for synonyms	There may be multiple synonyms and the model should allow for lists for the synonym attribute
8/17/2021	BZ	Add "mutation" as a DependsOn Component for animalModel	"mutation" is an FK in the animalModel table.
8/17/2021	BZ	Add link to the International Committee on Standardized Genetic Nomenclature for Mice in the strainNomenclature row.	For information and tracking purposes.
8/17/2021	BZ	Remove "atccId" and "cellosaurusId" from DependsOn for the cellLine table	RRID will be included and should be sufficient. Internally discussed this.
8/17/2021	BZ	Remove "cellType" from DependsOn for the cellLine table	Overlaps with cellLineCategory. Internally discussed this.
8/17/2021	BZ	Add "mutation" and dependsOn Component for the cellLine table	mutation is an FK of the cellLine table.
8/17/2021	BZ	Delete "atccId" and cellosaurusId" as attributes from schema.	Redundant to RRID. Internally discussed this.
8/17/2021	BZ	Add animalModel, cellLine, antibody, reagent, vendorItem to dependsOn Component for the Resource table	animalModel, cellLine, antibody, reagent, vendorItem are FKs in the Resource table.
8/17/2021	BZ	Add donor to dependsOn Component for the antibody table.	Donor is an FK in the anitbody table.
8/17/2021	BZ	Delete cellLine and animalModel from dependsOn Component for donor table.	It should be the opposite; animalModel and cellLine dependsOn Component donor
8/17/2021	BZ	Delete cellLine and animalModel from dependsOn Component for mutation table.	It should be the opposite; animalModel and cellLine dependsOn Component mutation.
8/17/2021	BZ	Put "list" in validation rules for proteinVariation, sequenceVariation, animalModelMutation, and animalMimicMutation.	These attribute will have more than one value.
8/17/2021	BZ	Put "list" in validation rules for specimenType, specimentTissueType, tumorType, disease, specimenPreparationMethod, and specimenFormat	These attribute will have more than one value.
8/17/2021	BZ	Add "developmentId" as an attribute and DependsOn for development	The development table as a unique identifier in the data model.
8/17/2021	BZ	Delete "resourceId," "investigatorId," "publicationId", and "funderId" from dependsOn for development	The dependsOn Component covers this conditional logic.
8/17/2021	BZ	Change "funderId" attribute to "funder", add "funderId" attribute and add "funderId: to dependsOn for funder.	Seemed to be a mistake, we left out funder but included funderId as the attribute defined as funder.
8/17/2021	BZ	Delete "development" as dependsOn Component for funder	Incorrect conditional logic. Development depends on Funder not the other way around.
8/17/2021	BZ	Delete "development" as dependsOn Component for investigator	Incorrect conditional logic. Development depends on Investigator not the other way around.
8/17/2021	BZ	Change investigatorId as TRUE for Required	PK must be required.
8/17/2021	BZ	Add description of investigatorSynapseId	To be consistent and thorough.
8/17/2021	BZ	Add publicationTitle, pmid, and doi as attributes. Add them as dependsOn for publication	Internal disucssions on adding these additional attributes.
8/17/2021	BZ	Delete development and resourceApplications as dependsOn Component for publication.	Incorrect conditional logic. Development and resourceApplications depends on publicaiton, not the other way around.
8/17/2021	BZ	Add "catalogNumberUrl" as an attribute and to dependsOn for vendorItem.	Internal disucssions on adding this additional attribute.
8/17/2021	BZ	Delete dependsOn Component Resource and add dependsOn Component vendor to vendorItem attribute	Conditional logic incorrect for resource. Resource dependsOn Component vendorItem, not the other way around. Vendor is an FK in vendorItem table, so should be dependsOn Component for vendorItem.
8/17/2021	BZ	Add "vendorId", "vendorUrl", and "vendorName" to dependsOn for vendor attribute	Vendor dependsOn these attributes.
8/17/2021	BZ	Delete vendorItem as dependsOn Component for vendor	Incorrect conditional logic. vendorItem dependsOn Component vendorItem, not the other way around.
8/17/2021	BZ	Add observationType, reliabilityRating, and easeOfUseRating	observationType, reliabilityRating, and easeOfUseRating were missing from spreadsheet, but are in the data model.
8/17/2021	BZ	Add resource as dependsOn Component for observation attribute	resource FK in observation table.
8/17/2021	BZ	Add reliabilityRating and easeOfUseRating as attributes	Was missing from schema.
8/17/2021	BZ	Add resource and publication as dependsOn Component for resourceApplication	resource and publication are FKs in the resourceApplication table.
8/17/2021	BZ	Add validation rules of "list" to llinks and graphics	May be more than one shareable link or graphic.
8/17/2021	BZ	Add resourceApplicationId as attribute	Missing from schema.
8/17/2021	BZ	Add transplantationDonorId as an attribute	To reference for DependsOn for animalModel table.
8/17/2021	BZ	Add all FK (ids) to dependsOn for components that have them listed in their respective tables.	Discussion with Milen says to include in DependsOn.
8/18/2021	RJA	Update definitions for easeOfUse and reliabilityRatings	To make clear what these attributes capture.
8/18/2021	RJA	Add controlled values for easeOfUse and reliabilityRatings	To set 1-5 range for these values.
8/18/2021	BZ	Delete donorType from dependsOn for donor attribute.	Previous discussions with James decided to delete this.
8/18/2021	BZ	Add observationSubmitterId as an attribute and DependsOn for observation.	Attribute is part of the data model.
8/18/2021	BZ	Set Required for investigatorName to TRUE	Attribute should be required.
8/18/2021	BZ	Delete "graphics" attribute.	Out of scope for prototype phase of the project. Users can submit links to graphics in the meantime.
8/19/2021	RJA	Released v1.0	n/a