MyGene MCP Server
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_field_statisticsD | Get statistics for a specific field. |
| query_genesC | Search for genes using the MyGene.info query API. |
| search_by_fieldC | Search by specific fields with boolean operators. |
| get_gene_annotationC | Get detailed annotation for a specific gene by ID. |
| get_genes_batchC | Get annotations for multiple genes in a single request. |
| query_genes_batchC | Query multiple genes in a single request. |
| query_genes_by_intervalB | Query genes by genomic interval (chromosome position). |
| get_available_fieldsA | Get a list of all available fields in MyGene.info. |
| get_mygene_metadataA | Get metadata about the MyGene.info API service. |
| get_species_listA | Get a list of all supported species in MyGene.info. |
| get_gene_expression_profileC | Get expression profile across tissues/cell types. |
| query_genes_by_expressionC | Query genes by expression patterns. |
| get_gene_pathwaysC | Get all pathways for a gene. |
| query_genes_by_pathwayC | Find genes in specific pathways. |
| get_gene_go_annotationsC | Get GO annotations with evidence codes. |
| query_genes_by_go_termC | Query genes by GO terms with evidence filtering. |
| get_gene_orthologsC | Get orthologs across species. |
| query_homologous_genesC | Find homologous genes across species. |
| get_gene_disease_associationsB | Get disease associations for a gene. |
| query_genes_by_diseaseC | Find genes associated with diseases. |
| get_gene_variantsC | Get variants from ClinVar and other sources. |
| get_gene_chemical_interactionsC | Get chemical/drug interactions for a gene. |
| query_genes_by_chemicalC | Find genes that interact with chemicals/drugs. |
| build_complex_queryC | Build complex boolean queries with filters and aggregations. |
| query_with_filtersD | Query with multiple filters applied. |
| export_gene_listD | Export gene data in various formats. |
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 26 tools
There are overlapping tools like query_homologous_genes and get_gene_orthologs, which both find cross-species homologs. Additionally, query_with_filters, build_complex_query, and search_by_field all appear to serve similar flexible querying purposes, causing confusion.
Most tools follow a consistent get_gene_* or query_genes_by_* pattern, but there are deviations such as query_with_filters, build_complex_query, search_by_field, and export_gene_list that break the convention. The mixing of verbs like query, search, and build adds inconsistency.
With 26 tools, the server exceeds the recommended range and feels heavy, even for a comprehensive gene API. While each tool may target a specific aspect, the sheer number makes it harder for agents to select the appropriate one.
The tool set covers a wide range of gene-related queries including diseases, chemicals, pathways, GO terms, expression, variants, and orthologs, with batch operations and export functionality. Minor redundancies exist but no obvious gaps for the MyGene.info domain.