Mousemine Tools

Configuration File: mousemine_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the mousemine_tools.json configuration file.

Available Tools

MouseMine_search (Type: BaseRESTTool)

Search MouseMine, the InterMine data warehouse for mouse (Mus musculus) genomics data from MGI (M…

MouseMine_search tool specification

Tool Information:

  • Name: MouseMine_search

  • Type: BaseRESTTool

  • Description: Search MouseMine, the InterMine data warehouse for mouse (Mus musculus) genomics data from MGI (Mouse Genome Informatics). Searches across genes, alleles, proteins, publications, gene ontology terms, protein domains, and more. Returns matching records with category facets and relevance scores. MouseMine integrates data from MGI including gene annotations, phenotypes, alleles, expression data, pathways, and disease models. Use facet_Category parameter to filter by specific entity type (e.g., ‘ProteinCodingGene’, ‘Allele’, ‘Publication’, ‘Protein’).

Parameters:

  • q (string) (required) Search query: gene symbol (e.g., ‘Brca1’, ‘Tp53’, ‘Sox9’), protein name, disease term, or free text.

  • size (integer) (optional) Number of results to return (default: 10, max: 100).

  • format (string) (optional) Response format. Must be ‘json’.

  • facet_Category (string) (optional) Filter results by entity category. Options include: ‘ProteinCodingGene’, ‘Gene’, ‘Allele’, ‘Protein’, ‘Publication’, ‘Genotype’, ‘GOTerm’, ‘ProteinDomain’, ‘GXDExpression’, ‘NcRNAGene’, ‘AntisenseLncRNAGene’, ‘Strain’, ‘HTExperiment’, ‘InteractionExperiment’, ‘DOTerm’, ‘UniProtFeature’.

Example Usage:

query = {
    "name": "MouseMine_search",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)

MouseMine_search_alleles (Type: BaseRESTTool)

Search MouseMine specifically for mouse alleles and mutants. Returns allele symbols, names, MGI i…

MouseMine_search_alleles tool specification

Tool Information:

  • Name: MouseMine_search_alleles

  • Type: BaseRESTTool

  • Description: Search MouseMine specifically for mouse alleles and mutants. Returns allele symbols, names, MGI identifiers, allele types (Targeted, Endonuclease-mediated, Spontaneous, etc.), and attribute strings (Null/knockout, etc.) from Mouse Genome Informatics (MGI). Useful for finding knockout/knockin alleles, spontaneous mutations, and transgenic alleles for specific genes. For broader searches, use MouseMine_search instead.

Parameters:

  • q (string) (required) Allele search query: gene symbol (e.g., ‘Brca1’), allele symbol (e.g., ‘Brca1<tm1Whl>’), or keyword.

  • size (integer) (optional) Number of results to return (default: 10).

Example Usage:

query = {
    "name": "MouseMine_search_alleles",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)

MouseMine_search_genes (Type: BaseRESTTool)

Search MouseMine specifically for mouse protein-coding genes. This is a convenience wrapper that …

MouseMine_search_genes tool specification

Tool Information:

  • Name: MouseMine_search_genes

  • Type: BaseRESTTool

  • Description: Search MouseMine specifically for mouse protein-coding genes. This is a convenience wrapper that filters results to ProteinCodingGene category only. Returns gene symbols, MGI identifiers, and organism information from Mouse Genome Informatics (MGI). For broader searches across all entity types, use MouseMine_search instead.

Parameters:

  • q (string) (required) Gene search query: gene symbol (e.g., ‘Brca1’, ‘Tp53’), gene name, or keyword.

  • size (integer) (optional) Number of results to return (default: 10).

Example Usage:

query = {
    "name": "MouseMine_search_genes",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)