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BioThings APIs
Multiple BioThings APIs are created and maintained by the Service Provider team to make knowledge-source data accessible through high-performance BioThings APIs. All knowledge-source data is "open-source", but please look at the licensing information for each individual knowledge-source for full details.
Each knowledge-source's data is:
- cleaned up and processed. The data is often organized by unique entity (ex: by individual gene) or by unique association (ex: unique combo of subject-predicate-object)
- put into individual APIs and hosted at https://biothings.transltr.io/
These BioThings APIs do not comply to the TRAPI standard. More information on how to query each API directly is provided in their SmartAPI registrations. Their individual pages in https://biothings.transltr.io/ also have examples of how to query each API directly.
However, in collaboration with the Exploring Agent team, these BioThings APIs are accessible as TRAPI KP services through:
- the
/team/and/smartapi/endpoints of BioThings Explorer (see SmartAPI registration for details) - the Service-Provider TRAPI registration
In these situations, BioThings Explorer acts as a "TRAPI wrapper/transformer" that queries the BioThings APIs and processes their responses into knowledge-graphs that follow TRAPI and biolink-model standards (for node categories, edge predicates, etc).
This list includes the server url for each BioThings API, the SmartAPI registration, and the Translator wiki page for the knowledge source.
- For these BioThings APIs: https://github.com/biothings/pending.api
- For BioThings Explorer: https://github.com/biothings/biothings_explorer
- paper on BioThings toolkit (SDK) used to create these APIs: https://doi.org/10.1093/bioinformatics/btac017
- BioThings Explorer paper: https://doi.org/10.1093/bioinformatics/btad570