README.md

Bioschemas specification releases

This repository archives the type and profile releases. As Bioschemas types and profiles are versioned independently, the files for types, draft types, and released profiles are distributed together using the release date also as version under the license CC-by-sa, same as schema.org. Draft profiles are not distributed as only the released profiles are used for validation and quality check purposes, e.g., by FAIR-checker.

Releases and files

Types and draft types are distributed as TTL and JSON-LD, while released profiles using SHACL, also in TTL and JSON-LD.

The latest version are always included on the Bioschemas website on the technical corner of types and profiles. They are also accessible directly:

• Types, with canonical URL https://bioschemas.org/terms/
  • Types TTL
  • Types JSON-LD
• Draft types, with canonical URL https://bioschemas.org/draft_terms
  • Draft types TTL
  • Draft types JSON-LD
• Profiles
  • Profiles SCHAL TTL
  • Profiles SCHAL JSON-LD

Processes

• First make sure that the specification files https://github.com/BioSchemas/specifications are up-to-date. They need to be updated based on modifications done in the DDE platform on individual types or profiles
• Whenever a profile is updated in https://github.com/BioSchemas/specifications, a process will be automatically triggered to update https://github.com/BioSchemas/bioschemas-dde. The profile-realted files that are synchronyzed are:
  • bioschemas.json
  • bioschemasdeprecated.json
  • bioschemasdrafts.json
• Whenever a type is updated in https://github.com/BioSchemas/specifications, it requires a manual update on https://github.com/BioSchemas/bioschemas-dde. The type-related files in DDE are:
  • bioschemastypes.json
  • bioschemastypesdrafts.json
• If everything is up-to-date in https://github.com/BioSchemas/bioschemas-dde, then run the scripts at https://github.com/BioSchemas/bioschemas.github.io/tree/master/notebooks.
  • BioschemasTypes.ipynb creates the TTL and JSON-LD for types and draft types. The files bioschemas_draft_types_temp.jsonld, bioschemas_draft_types_temp.ttl, bioschemas_types_temp.jsonld, and bioschemas_types_temp.ttl should be copied to https://github.com/BioSchemas/bioschemas.github.io/tree/master/pages/_types without the "_temp" part
  • Types will become available (once the PR is approved) at https://bioschemas.org/types/bioschemas_types.jsonld
  • BioschemasProfiles.ipynb uses https://bioschemas.org/types/bioschemas_types.jsonld and creates a HTML file per property under https://github.com/BioSchemas/bioschemas.github.io/tree/master/pages/_properties
  • BioschemasProperties.ipynb uses https://raw.githubusercontent.com/BioSchemas/bioschemas-dde/main/bioschemas.json and https://raw.githubusercontent.com/BioSchemas/bioschemas-dde/main/bioschemasdrafts.json to generate the SHACL files in TTL and JSON-LD what will be located at https://github.com/BioSchemas/bioschemas.github.io/tree/master/pages/_profiles