AGR 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
} |
| resources | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_genesC | Search for genes across all Alliance of Genome Resources model organisms. Supports species filtering. |
| get_gene_infoA | Get detailed information about a specific gene including symbol, name, location, species, and cross-references. |
| get_gene_diseasesA | Get disease associations for a gene, including human disease models and annotations. |
| search_diseasesC | Search for diseases in the Alliance database. |
| get_gene_expressionC | Get expression data for a gene including tissue/cell type expression and developmental stages. |
| find_orthologsB | Find orthologous genes across species. Returns homologs from all Alliance model organisms. |
| get_gene_phenotypesC | Get phenotype annotations for a gene. |
| get_gene_interactionsC | Get molecular and genetic interactions for a gene. |
| get_gene_allelesB | Get alleles/variants associated with a gene. |
| search_allelesC | Search for alleles/variants in the Alliance database. |
| get_species_listB | Get list of model organisms supported by Alliance of Genome Resources. |
| mine_searchC | Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search. |
| mine_queryA | Run a raw PathQuery XML query against AllianceMine. For power users who know InterMine PathQuery syntax. |
| mine_query_builderA | Build and run structured queries against AllianceMine using a JSON DSL. Example query - find human genes in DNA repair pathway: { "from": "Gene", "select": ["symbol", "name", "organism.name", "pathways.name"], "where": { "organism.name": "Homo sapiens", "pathways.name": { "op": "CONTAINS", "value": "DNA repair" } }, "limit": 50 } Supported operators: =, !=, CONTAINS, LIKE, <, >, <=, >=, ONE OF, NONE OF, IS NULL, IS NOT NULL |
| mine_natural_queryB | Process a natural language query and return schema information to construct a structured AllianceMine query. This tool returns the AllianceMine schema so you can convert the user's natural language into a mine_query_builder call. |
| mine_list_templatesB | List available query templates in AllianceMine. Templates are pre-built queries for common use cases. |
| mine_run_templateA | Run a pre-built query template with parameters. Parameter format: Use numeric keys ("1", "2", etc.) matching constraint positions.
Common templates:
Use mine_list_templates to discover all available templates and their constraints. |
| mine_get_listsC | Get all available gene/protein lists in AllianceMine. |
| mine_get_listC | Get the contents of a specific list. |
| mine_create_listC | Create a new list in AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable. |
| mine_add_to_listC | Add items to an existing list. Requires ALLIANCEMINE_TOKEN environment variable. |
| mine_delete_listC | Delete a list from AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| entity-types | |
| species |
TDQS
Scored across 22 tools
Most tools have distinct purposes, but there is some overlap between search_genes and find_orthologs (both involve gene-related queries across species), and between mine_query, mine_query_builder, and mine_natural_query (all for querying AllianceMine, though they differ in input format). The descriptions help clarify these distinctions, but an agent might occasionally misselect between them.
The naming is mostly consistent with a verb_noun pattern (e.g., get_gene_info, search_genes, mine_create_list), but there are minor deviations like mine_natural_query (which uses 'natural' as an adjective) and the mix of 'get' vs. 'search' prefixes for similar actions. Overall, the pattern is predictable and readable.
With 22 tools, the count feels borderline heavy for a genomics server, though it covers both gene data retrieval and AllianceMine operations. It might overwhelm agents with too many options, but the scope is broad enough to justify a larger set, making it reasonable but not ideal.
The tool set provides comprehensive coverage for the domain of genomic data and AllianceMine interactions. It includes CRUD operations for lists (create, get, delete, add), extensive gene data retrieval (info, expression, diseases, etc.), and multiple query methods (search, templates, natural language, structured), leaving no obvious gaps for agent workflows.