NCBI Genetic Testing Registry¶
NCBI Genetic Testing Registry (GTR) is the right source when you need gene-centric genetic tests, laboratory offerings, testing methods, or condition-linked diagnostics. In BioMCP, GTR is the local-runtime backbone for the multi-source diagnostic entity: search diagnostic --source gtr stays on the NCBI bundle, while the default --source all route can merge GTR rows with WHO IVD rows and keeps source provenance visible.
BioMCP auto-downloads the GTR test_version.gz and test_condition_gene.txt bulk exports into BIOMCP_GTR_DIR or the default platform data directory on first diagnostic use, refreshes stale data after 7 days, reports GTR local data (<root>) in full health output, and exposes biomcp gtr sync for forced refreshes.
What BioMCP exposes¶
| Command | What BioMCP gets from this source | Integration note |
|---|---|---|
search diagnostic --gene <symbol> --source gtr |
Gene-linked genetic test rows | Uses the local GTR condition/gene relation bundle for gene-centric lookup |
search diagnostic --disease <name> --source gtr |
Condition-linked GTR diagnostic rows | Applies the same bounded disease phrase matching used by the multi-source diagnostic route |
search diagnostic --type <method> --source gtr |
GTR testing-method filtered rows | Matches source-native GTR methods |
search diagnostic --manufacturer <name> --source gtr |
Laboratory or provider filtered rows | Filters over GTR lab/provider metadata when available |
get diagnostic GTR000006692.3 |
Source-native GTR diagnostic summary card | GTR accessions are the detail identifiers |
get diagnostic GTR000006692.3 genes |
Joined gene symbols for the test | JSON keeps the full deduped symbol arrays even when markdown rows are compact |
get diagnostic GTR000006692.3 conditions |
Joined condition names for the test | Preserves GTR condition provenance |
get diagnostic GTR000006692.3 methods |
GTR source-native testing methods | GTR supports genes, conditions, methods, and opt-in regulatory overlay sections |
biomcp health |
GTR local readiness row | Reports whether the local bundle is configured, stale, missing, or available at the default path |
biomcp gtr sync |
Explicit GTR refresh | Force-refreshes the local GTR bulk files |
Example commands¶
Returns GTR genetic-test rows linked to BRCA1 with accession IDs ready for get diagnostic.
Searches GTR condition-linked diagnostic rows using the bounded disease phrase filter.
Fetches a source-native GTR diagnostic card with the main GTR-supported detail sections.
Force-refreshes the local GTR bulk bundle without waiting for the next automatic refresh.
Shows the GTR local data readiness row alongside WHO IVD and the other local-runtime bundles.
API access¶
No BioMCP API key required. BioMCP auto-downloads the public GTR bulk files into
BIOMCP_GTR_DIR or the default data directory on first use. The optional
regulatory section for diagnostic cards is an OpenFDA device overlay and can
benefit from OPENFDA_API_KEY; base GTR search and detail do not require a key.
Official source¶
NCBI Genetic Testing Registry is the official NCBI diagnostic-test registry behind BioMCP's GTR-backed diagnostic workflow. BioMCP reads the public bulk export at https://ftp.ncbi.nlm.nih.gov/pub/GTR/data/.