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Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

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

CapabilityDetails
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

NameDescription
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Report the local HGNC index status: whether the data is built, the loaded release date, gene/withdrawn counts, schema version, and when it was built.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 Accepts a current symbol, a previous (withdrawn) symbol, an alias, or an HGNC id in either form (HGNC:1100 or 1100), case-insensitively.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 An alias shared by several genes returns an ambiguous_query error with the candidate list (not silently picked); a withdrawn/merged symbol returns a not_found error that redirects to the successor record.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

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription
capabilities
tools_overview
usage
reference
research_use
citation

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