Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| resources | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_genes | Search for genes across all Alliance of Genome Resources model organisms. Supports species filtering. |
| get_gene_info | Get detailed information about a specific gene including symbol, name, location, species, and cross-references. |
| get_gene_diseases | Get disease associations for a gene, including human disease models and annotations. |
| search_diseases | Search for diseases in the Alliance database. |
| get_gene_expression | Get expression data for a gene including tissue/cell type expression and developmental stages. |
| find_orthologs | Find orthologous genes across species. Returns homologs from all Alliance model organisms. |
| get_gene_phenotypes | Get phenotype annotations for a gene. |
| get_gene_interactions | Get molecular and genetic interactions for a gene. |
| get_gene_alleles | Get alleles/variants associated with a gene. |
| search_alleles | Search for alleles/variants in the Alliance database. |
| get_species_list | Get list of model organisms supported by Alliance of Genome Resources. |
| mine_search | Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search. |
| mine_query | Run a raw PathQuery XML query against AllianceMine. For power users who know InterMine PathQuery syntax. |
| mine_query_builder | 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_query | 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_templates | List available query templates in AllianceMine. Templates are pre-built queries for common use cases. |
| mine_run_template | 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_lists | Get all available gene/protein lists in AllianceMine. |
| mine_get_list | Get the contents of a specific list. |
| mine_create_list | Create a new list in AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable. |
| mine_add_to_list | Add items to an existing list. Requires ALLIANCEMINE_TOKEN environment variable. |
| mine_delete_list | 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 |