biocontext
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_API_KEY | No | Optional NCBI Entrez API key. Raises rate limit from 3 to 10 requests per second. |
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": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| resolve_geneA | Resolve an ambiguous gene symbol, alias, or accession to an authoritative entity. Args: query: Gene symbol (e.g. TP53), alias (e.g. HER2, p53), or accession. taxon_id: NCBI Taxonomy ID (default: 9606 for human). chromosome: Optional chromosome hint for disambiguation (e.g. '17' or 'chr17'). locus_type: Optional biotype hint (e.g. 'protein-coding', 'pseudogene'). Returns: JSON string containing the resolved canonical gene entity, cross-references, and match audit trail. |
| get_protein_infoA | Fetch structured protein details from UniProt by primary accession. Args: accession: UniProt accession ID (e.g. P04637). Returns: JSON string containing protein name, gene, length, mass, and organism. |
| batch_resolve_genesA | Resolve a list of gene identifiers/aliases in batch. Args: queries: List of gene symbols or aliases (e.g. ["TP53", "HER2", "EGFR"]). taxon_id: NCBI Taxonomy ID (default: 9606 for human). Returns: JSON string containing list of resolved entity results. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 3 tools
Tools are largely distinct: get_protein_info fetches protein details by accession, while resolve_gene and batch_resolve_genes both handle gene resolution. The overlap between single and batch resolution is clear from descriptions, so an agent can choose appropriately without much confusion.
All tool names follow a consistent verb_noun pattern: get_protein_info, batch_resolve_genes, resolve_gene. Even the batch_ prefix maintains a clear convention, making the naming uniform and predictable.
With only 3 tools, the server is minimal but well-scoped for the domain of gene and protein resolution. While it's on the lower end of typical counts, the tools cover core operations for this focused purpose, so the count feels appropriate rather than thin.
The server covers single and batch gene resolution plus protein lookup by accession, but lacks operations like batch protein retrieval or direct gene-to-protein mapping. Agents may need to chain resolve_gene and get_protein_info manually, representing a notable gap in seamless workflow completion.