Search for genes across all Alliance of Genome Resources model organisms. Supports species filtering.

Get detailed information about a specific gene including symbol, name, location, species, and cross-references.

Get disease associations for a gene, including human disease models and annotations.

Search for diseases in the Alliance database.

Get expression data for a gene including tissue/cell type expression and developmental stages.

Find orthologous genes across species. Returns homologs from all Alliance model organisms.

Get phenotype annotations for a gene.

Get molecular and genetic interactions for a gene.

Get alleles/variants associated with a gene.

Search for alleles/variants in the Alliance database.

Get list of model organisms supported by Alliance of Genome Resources.

Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search.

Run a raw PathQuery XML query against AllianceMine. For power users who know InterMine PathQuery syntax.

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

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.

List available query templates in AllianceMine. Templates are pre-built queries for common use cases.

Run a pre-built query template with parameters.

Parameter format: Use numeric keys ("1", "2", etc.) matching constraint positions.

• Simple: {"1": "BRCA1"} - just the value

• Full: {"1": {"path": "Gene", "op": "LOOKUP", "value": "BRCA1"}}

Common templates:

• Gene_Orthologs: Find orthologs (params: {"1": {"path": "Gene", "op": "LOOKUP", "value": "HGNC:1100"}})

• Gene_GOTerms: GO annotations for a gene

• Gene_DOTerm: Disease annotations for a gene

• GOTerm_Genes: Find genes by GO term

Use mine_list_templates to discover all available templates and their constraints.

Get all available gene/protein lists in AllianceMine.

Get the contents of a specific list.

Create a new list in AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable.

Add items to an existing list. Requires ALLIANCEMINE_TOKEN environment variable.

Delete a list from AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable.