Alliance Genome Tools

Configuration File: alliance_genome_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

Alliance_get_disease (Type: AllianceGenomeTool)

Get disease summary information from the Alliance of Genome Resources by Disease Ontology (DO) ID…

Alliance_get_disease tool specification

Tool Information:

  • Name: Alliance_get_disease

  • Type: AllianceGenomeTool

  • Description: Get disease summary information from the Alliance of Genome Resources by Disease Ontology (DO) ID. Returns disease name, definition, synonyms, and classification. The Alliance integrates disease annotations from multiple model organism databases. Example: ‘DOID:162’ returns cancer with definition and synonyms like ‘malignant neoplasm’.

Parameters:

  • disease_id (string) (required) Disease Ontology (DO) ID. Examples: ‘DOID:162’ (cancer), ‘DOID:10652’ (Alzheimer’s disease), ‘DOID:9351’ (diabetes mellitus), ‘DOID:1612’ (breast cancer).

Example Usage:

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

Alliance_get_disease_genes (Type: AllianceGenomeTool)

Get genes associated with a disease across all model organisms from the Alliance of Genome Resour…

Alliance_get_disease_genes tool specification

Tool Information:

  • Name: Alliance_get_disease_genes

  • Type: AllianceGenomeTool

  • Description: Get genes associated with a disease across all model organisms from the Alliance of Genome Resources. Uses Disease Ontology (DO) IDs to find genes linked to a disease from human, mouse, rat, zebrafish, fly, worm, and other organisms. Includes both direct annotations and inferred associations from model organism phenotypes. Example: ‘DOID:162’ (cancer) returns TP53, BRCA1, and thousands more.

Parameters:

  • disease_id (string) (required) Disease Ontology (DO) ID. Examples: ‘DOID:162’ (cancer), ‘DOID:10652’ (Alzheimer’s disease), ‘DOID:9351’ (diabetes mellitus), ‘DOID:1612’ (breast cancer).

  • limit (integer) (optional) Maximum number of gene associations to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

Example Usage:

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

Alliance_get_gene (Type: AllianceGenomeTool)

Get detailed gene information from the Alliance of Genome Resources, which integrates data from 7…

Alliance_get_gene tool specification

Tool Information:

  • Name: Alliance_get_gene

  • Type: AllianceGenomeTool

  • Description: Get detailed gene information from the Alliance of Genome Resources, which integrates data from 7 model organism databases (SGD, FlyBase, WormBase, ZFIN, RGD, MGI, Xenbase) plus human. Returns gene symbol, name, species, synopsis, synonyms, genomic location, and cross-references. Example: ‘HGNC:6081’ returns insulin gene info.

Parameters:

  • gene_id (string) (required) Alliance gene ID with source prefix. Examples: ‘HGNC:6081’ (human INS), ‘MGI:98834’ (mouse Trp53), ‘FB:FBgn0003996’ (fly w), ‘SGD:S000000259’ (yeast GAL4), ‘ZFIN:ZDB-GENE-990415-8’ (zebrafish pax2a), ‘WB:WBGene00006763’ (worm unc-13).

Example Usage:

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

Alliance_get_gene_phenotypes (Type: AllianceGenomeTool)

Get phenotype annotations for a gene from the Alliance of Genome Resources. Returns phenotypes ob…

Alliance_get_gene_phenotypes tool specification

Tool Information:

  • Name: Alliance_get_gene_phenotypes

  • Type: AllianceGenomeTool

  • Description: Get phenotype annotations for a gene from the Alliance of Genome Resources. Returns phenotypes observed when the gene is mutated or knocked out, aggregated from model organism databases. Supports all model organisms (yeast, fly, worm, zebrafish, mouse, rat, frog). Example: ‘HGNC:6081’ (INS) returns phenotypes like ‘Abnormal circulating insulin concentration’.

Parameters:

  • gene_id (string) (required) Alliance gene ID with source prefix. Examples: ‘HGNC:6081’ (human INS), ‘MGI:98834’ (mouse Trp53), ‘FB:FBgn0003996’ (fly w).

  • limit (integer) (optional) Maximum number of phenotypes to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

Example Usage:

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

Alliance_search_genes (Type: AllianceGenomeTool)

Search for genes across all model organisms in the Alliance of Genome Resources. Searches by gene…

Alliance_search_genes tool specification

Tool Information:

  • Name: Alliance_search_genes

  • Type: AllianceGenomeTool

  • Description: Search for genes across all model organisms in the Alliance of Genome Resources. Searches by gene symbol, name, or keyword and returns matching genes from human, mouse, rat, zebrafish, fly, worm, yeast, and frog databases. Provides type-ahead suggestions. Example: ‘insulin’ returns INS (human), Ins1/Ins2 (mouse), ins (zebrafish), etc.

Parameters:

  • query (string) (required) Gene name, symbol, or keyword to search for. Examples: ‘insulin’, ‘tumor protein p53’, ‘hedgehog’, ‘notch’.

  • limit (integer) (optional) Maximum number of results to return (1-50). Default: 10.

Example Usage:

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