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 one page of each category with true totals and explicit continuation metadata; while metadata.has_more is true, pass metadata.next_page as page with the same filters. Returns allele/variant records with HGVS genomic locations and disease/phenotype flags, plus affected genomic models (genotypes/strains).

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).

  • page (integer) (optional) One-based page number shared by the allele and model queries. Continue with metadata.next_page while metadata.has_more is true.

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 Ontology term across model organisms. Results are recoverably…

Alliance_get_disease_genes tool specification

Tool Information:

  • Name: Alliance_get_disease_genes

  • Type: AllianceGenomeTool

  • Description: Get genes associated with a Disease Ontology term across model organisms. Results are recoverably paginated: start with page=1 and continue with metadata.next_page while metadata.has_more is true; metadata.total_results and total_pages are exact.

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, including species, synopsis,…

Alliance_get_gene tool specification

Tool Information:

  • Name: Alliance_get_gene

  • Type: AllianceGenomeTool

  • Description: Get detailed gene information from the Alliance of Genome Resources, including species, synopsis, synonyms, genomic location, and paginated cross-references. Use xref_offset/xref_limit and inspect cross_references_total, cross_references_truncated, and next_xref_offset; well-studied genes can have hundreds of cross-references.

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).

  • xref_offset (integer) (optional) Zero-based cross-reference offset.

  • xref_limit (integer) (optional) Cross-references returned per page (default 10, maximum 500).

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 one page of each category with true totals and explicit continuation metadata; while metadata.has_more is true, pass metadata.next_page as page with the same filters. 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.

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).

  • page (integer) (optional) One-based page number shared by the ortholog and paralog queries. Continue with metadata.next_page while metadata.has_more is true.

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. Results are recoverab…

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. Results are recoverably paginated: start with page=1 and continue with metadata.next_page while metadata.has_more is true; metadata.total_results and total_pages are exact.

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, including …

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, including evidence references. Results are recoverably paginated: start with page=1 and continue with metadata.next_page while metadata.has_more is true; metadata.total_results and total_pages are exact.

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 genes across all Alliance of Genome Resources species by symbol, synonym, name, or keyword…

Alliance_search_genes tool specification

Tool Information:

  • Name: Alliance_search_genes

  • Type: AllianceGenomeTool

  • Description: Search genes across all Alliance of Genome Resources species by symbol, synonym, name, or keyword. Returns exact total_results and recoverable offset pagination; continue with next_offset while has_more is true. Results include human, mouse, rat, zebrafish, fly, worm, yeast, and frog genes. Example: ‘TP53’ has more than 100 cross-species and related gene matches.

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.

  • offset (integer) (optional) Zero-based offset in the complete matching gene list. Continue with metadata.next_offset. Default: 0.

Example Usage:

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