Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
**Added** * Add Study Key to all schemas * Add "Component" Key attributes to shared and in relevant schemas (e.g., Biospecimen Key, ImagingLevel1 Key, etc.). Keys use cross-manifest validation. * Add Data Use Codes attribute to File View and Dataset View models; component-specific Data Use Codes to Study and Sharing Plans * Add attributes and schemas for Collections, Model, Individual, Imaging (Level 1 - 4 and Channel), Sequencing (Level 1- 3, derived from CDS, GeoMx, Visium, and Shared), and RNA Sequencing (Level 1) * Add CDS attributes to Biospecimen and Study schemas (e.g., Primary Diagnosis, ) * Add longitudinal attributes to File View schema * Add controlled vocabulary terms associated with CDS attributes * Add controlled vocab terms from Data Sharing Pilots - "Whole Animal" as specimen type - "Light Sheet Microscopy" as an assay type **Updates** * Update DSP attributes and schema - Add keys, governance, and CDS-related attributes (e.g, DSP IRB Form attribute, ) - Additional attributes are intended to provide governance and CDS-related submission information - DataDSP schema should now approximate features in the DSP google doc, aside from written instructions. * Update ToolView attributes * Update species controlled vocabulary to include more human-related terms **Removed** * Remove unused schemas: Consortium Grant, Dataset, Dataset Grant, Grant, Institution Grant, Person Consortium, Publication, Publication View DCA, Theme Grant, Tool, Tool Grant, * Change Tumor Type to Disease Type for experimental metadata that will be sent to CDS/Data Hub - Will be mapped to existing tumor types for annotation purposes, Disease Type is requested by CDS * Update release_workflow.sh: Add template types, Change output type to CSV (-o flag) and generate google sheets (-s flag) * Replace old XLSX templates with CSVs: Generated with release_workflow.sh * Update GeoMx schema definitions - Remove Parent Biospecimen ID attribute - Remove Filename as GeoMx-specific attribute, since it is now shared - Label GeoMx-specific File Format * Remove Tumor Subtype valid values, to be replaced by an expanded set of subtypes at a later date **Organization** * Separate assay-specific models into level folders * Move attributes and controlled vocab to relevant module subfolders - Terms associated with a model component/introduced in a component will be defined in the annotationProperty.csv of the component - Controlled vocab associated with the attribute is stored in the module/component subfolder - The annotationProperty.csv in module/shared is reserved for generalized attributes that are intended to be used across many schemas (e.g., Data Use Codes, Component Keys, Workflow Link, etc.) * Relocate RNA-specific attributes: Sequencing Level 1 - 3 will serve as a broad sequencing assay template. Sub models will be added that contain more specific information types. SequencingRNALevel1 will surface RNA-seq focused metadata elements for raw/unprocessed data * Replace commas in CDS terms with semicolons - Addresses an issue with terms being incorrectly read when valid values are parsed from CSV format * Update build-jsonld.yml - bump schematicpy to 24.10.2 * Update release_workflow.sh: Add additional templates to datatypes and add an 'if' statement to control make. Model conversion is taking ~16 minutes, so we only want to run that when necessary. * Retain json data model schemas in model: Schemas can be bound to entities in Synapse via the client
- Loading branch information
