hgnc-link
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| logging | {} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| extensions | {
"io.modelcontextprotocol/ui": {}
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| get_server_capabilitiesA | Return the hgnc-link discovery surface. detail='summary' (default) is light: identity/build/HGNC release, the tool list WITH call signatures, accepted argument aliases, response modes, recommended workflows, error taxonomy, and limits. detail='full' adds vocabularies (locus groups, status values, match types) and the cross-reference database catalogue. Call this first in a cold session, or read hgnc://tools / hgnc://capabilities. Signature: get_server_capabilities(detail=). |
| get_hgnc_diagnosticsA | Report the local HGNC index status: whether the data is built, the loaded release date, gene/withdrawn counts, schema version, and when it was built. Use this to confirm freshness or diagnose an unavailable-data error. Signature: get_hgnc_diagnostics(). |
| resolve_symbolA | Resolve any gene symbol or HGNC id to its canonical record. Accepts a current symbol, a previous (withdrawn) symbol, an alias, or an HGNC id in either form (HGNC:1100 or 1100), case-insensitively. Returns {hgnc_id, approved_symbol, match_type (hgnc_id|current|previous|alias)}. An alias shared by several genes returns an ambiguous_query error with the candidate list (not silently picked); a withdrawn/merged symbol returns a not_found error that redirects to the successor record. Signature: resolve_symbol(query, response_mode=). |
| resolve_symbols_batchA | Resolve a batch of gene symbols / HGNC ids in one call (max 200). Each entry is resolved with the same current->previous->alias cascade as resolve_symbol; an individual miss or withdrawal never fails the batch (it is marked unresolved / obsolete in that entry). Returns per-query results plus resolved/unresolved counts. Signature: resolve_symbols_batch(queries, response_mode=). |
| get_geneA | Return the full HGNC record for a gene, resolved from an HGNC id, current symbol, previous symbol, or alias. Includes name, status, locus group/type, location, aliases/previous symbols, gene groups, and all cross-references. response_mode controls verbosity (compact drops dates/provenance; minimal keeps identity + anchor ids). Signature: get_gene(query, response_mode=). |
| search_genesA | Free-text search over gene symbols, names, aliases, and previous symbols (FTS, relevance-ranked). Returns ranked {hgnc_id, symbol, name, locus_type, score} summaries. Nomenclature-only: there is NO disease/phenotype semantics, so a descriptive query (e.g. 'polycystin kidney') only matches words present in a gene's nomenclature. Use resolve_symbol for an exact symbol/id; use this for partial names. Signature: search_genes(query, limit=, response_mode=). |
| get_gene_cross_referencesA | Return external database cross-references for a gene (forward identifier mapping): NCBI Gene, Ensembl, UniProt, RefSeq, MANE Select, OMIM, UCSC, VEGA, CCDS, MGI, RGD, Orphanet, COSMIC, PubMed. response_mode sets the default field set: minimal=NCBI+Ensembl ids; compact (default)=the high-value ids (NCBI, Ensembl, UniProt, RefSeq, MANE Select, OMIM, CCDS); standard/full=every populated field. databases optionally filters to specific sources by field key OR friendly label (e.g. 'mane', 'ncbi', 'uniprot') and OVERRIDES the response_mode tier; an unknown key is rejected with invalid_input + did-you-mean. Resolve the gene from an id/symbol/alias first. Signature: get_gene_cross_references(query, databases=, response_mode=). |
| resolve_gene_by_xrefA | Reverse identifier mapping: find the HGNC gene(s) for an external database id. source is the database (entrez_id/ncbi, ensembl_gene_id, uniprot, refseq, mane_select, omim, ucsc, vega, ccds, mgi, rgd) and value is the id (e.g. source='ensembl_gene_id', value='ENSG00000157764'). A version suffix is tolerated (ENSG00000012048.23 resolves like ENSG00000012048), and a MANE Select transcript (ENST…/NM_…) resolves back to its gene. Signature: resolve_gene_by_xref(source, value, response_mode=). |
| get_gene_groupA | Browse a HGNC gene group/family by numeric group id (e.g. '1157') or by name (e.g. 'RAF family'). Returns the member genes as symbol-ordered summaries. Members are paginated with limit + offset; the response carries member_count, returned, truncated, and next_offset, and (when truncated) a next_commands entry that fetches the next page. A name matching several groups returns the candidate groups so you can re-call with a specific id. Signature: get_gene_group(group, limit=, offset=, response_mode=). |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| capabilities | |
| tools_overview | |
| usage | |
| reference | |
| research_use | |
| citation |
TDQS
Scored across 9 tools
All nine tools have clearly distinct purposes: gene retrieval, cross-references, group browsing, diagnostics, capabilities, reverse lookup, single/batch symbol resolution, and free-text search. There is no overlap or ambiguity between any two tools.
Tool names follow a consistent verb_noun pattern (e.g., get_gene, resolve_symbol, search_genes). The verbs are either get, resolve, or search, each clearly indicating the action, and the nouns specify the target. No mixing of conventions.
With 9 tools, the server is well-scoped for the HGNC nomenclature domain. Each tool serves a distinct and necessary function (lookup, batch, search, cross-references, etc.), and the count is neither too sparse nor overwhelming.
The tool surface covers all core operations for a gene nomenclature service: single and batch resolution, forward and reverse cross-reference mapping, group browsing, free-text search, and server diagnostics/capabilities. There are no obvious missing operations for the stated purpose.