Alliance Genome Tools

Configuration File: alliance_genome_tools.json Tool Type: Local Tools Count: 8

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

Available Tools

Alliance_get_alleles_and_models (Type: AllianceGenomeTool)

Get alleles/variants and affected genomic models (mutant strains) for a gene via the Alliance of …

Alliance_get_alleles_and_models tool specification

Tool Information:

• Name: Alliance_get_alleles_and_models

• Type: AllianceGenomeTool

• Description: Get alleles/variants and affected genomic models (mutant strains) for a gene via the Alliance of Genome Resources (mouse/MGI, frog/Xenbase, and other members). Returns allele/variant records with HGVS genomic locations and disease/phenotype flags, plus affected genomic models (genotypes/strains). Example: MGI:97490 (Pax6) returns variant_summary records such as rs231853465 (NC_000068.8:g.105516528T>C) and models such as AffectedGenomicModel MGI:2680573.

Parameters:

• gene_id (string) (required) Alliance gene ID with member prefix, e.g. ‘MGI:97490’ (Pax6), ‘HGNC:8620’.

• limit ([‘integer’, ‘null’]) (optional) Max results per category (default 20, max 100).

Example Usage:

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

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_orthologs (Type: AllianceGenomeTool)

Get orthologs and paralogs of a gene across model organisms via the Alliance of Genome Resources …

Alliance_get_gene_orthologs tool specification

Tool Information:

• Name: Alliance_get_gene_orthologs

• Type: AllianceGenomeTool

• Description: Get orthologs and paralogs of a gene across model organisms via the Alliance of Genome Resources (used by MGI, Xenbase, and other members). Returns the stringent ortholog set with per-ortholog disease/expression annotation flags and prediction methods, plus the paralog set. Gene IDs use member prefixes (MGI:, HGNC:, RGD:, ZFIN:, FB:, WB:, SGD:, Xenbase:); bare WBGene/FBgn/MGI numeric IDs are auto-prefixed. Example: MGI:97490 (Pax6) returns gene_to_gene_orthology orthologs (e.g. Drosophila ey) and paralogs.

Parameters:

• gene_id (string) (required) Alliance gene ID with member prefix, e.g. ‘MGI:97490’ (Pax6), ‘HGNC:8620’, ‘RGD:3889’, ‘Xenbase:XB-GENE-865965’.

• stringency ([‘string’, ‘null’]) (optional) Ortholog stringency filter: ‘stringent’ (default), ‘moderate’, or ‘all’.

• limit ([‘integer’, ‘null’]) (optional) Max results per category (default 20, max 100).

Example Usage:

query = {
    "name": "Alliance_get_gene_orthologs",
    "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_get_molecular_interactions (Type: AllianceGenomeTool)

Get molecular (physical) interactions for a gene via the Alliance of Genome Resources (mouse/MGI,…

Alliance_get_molecular_interactions tool specification

Tool Information:

• Name: Alliance_get_molecular_interactions

• Type: AllianceGenomeTool

• Description: Get molecular (physical) interactions for a gene via the Alliance of Genome Resources (mouse/MGI, frog/Xenbase, and other members). Returns interactor gene IDs/symbols/species, interaction type, and supporting evidence references (PubMed / member curie). Gene IDs use member prefixes. Example: MGI:97490 (Pax6) returns gene_molecular_interaction records with evidence references such as MGI:6822438 (PMID:22863532).

Parameters:

• gene_id (string) (required) Alliance gene ID with member prefix, e.g. ‘MGI:97490’ (Pax6), ‘HGNC:8620’.

• limit ([‘integer’, ‘null’]) (optional) Max results (default 20, max 100).

• page ([‘integer’, ‘null’]) (optional) Page number (default 1).

Example Usage:

query = {
    "name": "Alliance_get_molecular_interactions",
    "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. Matches 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. Matches by gene symbol or synonym (type-ahead) and returns genes from human, mouse, rat, zebrafish, fly, worm, yeast, and frog databases. Use the official gene symbol rather than a descriptive name: ‘INS’ returns INS (human), Ins1/Ins2 (rat), ins (zebrafish), whereas ‘insulin’ matches GO terms/diseases, not genes.

Parameters:

• query (string) (required) Gene symbol or synonym to search for (not a descriptive name). Examples: ‘INS’, ‘TP53’, ‘shh’, ‘notch1’.

• 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)

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