mine_query_builder
Build structured queries to extract genomics data from AllianceMine using a JSON-based query language. Query genes, proteins, diseases, pathways, and phenotypes across multiple model organisms.
Instructions
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
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| from | Yes | Root class: Gene, Protein, Disease, Pathway, Phenotype, etc. | |
| select | Yes | Fields to return, e.g., ['symbol', 'organism.name'] | |
| where | No | Constraints as field: value or field: {op, value} | |
| joins | No | OUTER JOIN paths for optional relationships | |
| sort | No | Sort order | |
| limit | No | Maximum results |