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Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

No arguments

Capabilities

Features and capabilities supported by this server

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Report the local HGNC index status: whether the data is built, the loaded release date, gene/withdrawn counts, schema version, and when it was built.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 a data_unavailable 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 Accepts a current symbol, a previous (withdrawn) symbol, an alias, or an HGNC id in either form (HGNC:1100 or 1100), case-insensitively.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 An alias shared by several genes returns an ambiguous_query error with the candidate list (not silently picked); a withdrawn/merged symbol returns a not_found error that redirects to the successor record.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, omim, ucsc, vega, ccds, mgi, rgd) and value is the id (e.g. source='ensembl_gene_id', value='ENSG00000157764'). 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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