Releases: nf-osi/nf-research-tools-schema
Releases · nf-osi/nf-research-tools-schema
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
Full Changelog: v3.0.0...v4.0.0
Contributors
allaway, brynnz22, and cconrad8
Assets 2
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
Contributors
allaway and brynnz22
Assets 2
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 |