BioMedical Terminology Service for Cafe Variome
This service contains data for various biomedical terminologies, ontologies, and vocabularies. It serves as a centralised API for data services such as Cafe Variome to retrieve vocabulary information and aid user experience.
About
The BioMedical Terminology Service is designed to facilitate access to and usage of biomedical terminologies, ontologies, and vocabularies. It offers a centralised service, exposed through REST, GraphQL, FHIR, and MCP interfaces, that allows users and applications to query, retrieve, and interact with a wide range of biomedical terminological resources in various use cases, including research, clinical applications, and data analysis.
Features
On top of the normal searching and querying functionalities on biomedical terminologies, this service also provides advanced features:
- Unified access to multiple terminologies, ontologies, and vocabularies, including SNOMED CT, CTV3, HGNC, HPO, MONDO, NCIt, OMIM, ORDO, Reactome, Ensembl, and OHDSI.
- Parent-child and other relationship traversal, for use in external queries.
- Inter- and intra-vocabulary mapping for normalising subject tagging.
- Semantic similarity based searches and translations between term sets, backed by multiple pluggable similarity methods.
- Auto-complete and full-text search across loaded vocabularies.
- A GraphQL endpoint for fine-grained, client-selected field access, alongside the REST API.
- A FHIR-compatible terminology server interface, for interoperability with FHIR-based clinical systems.
- An MCP server, for use with LLMs and agents.
- Regular updates to ensure access to the latest versions of terminological resources.
- Comprehensive documentation and usage examples.
See the full documentation for installation instructions, API usage guides, and the mathematical background of the similarity methods.