Wormbase Tools

Configuration File: wormbase_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

WormBase_get_expression (Type: WormBaseTool)

Get expression data for a C. elegans gene from WormBase. Returns tissues where the gene is expres…

WormBase_get_expression tool specification

Tool Information:

  • Name: WormBase_get_expression

  • Type: WormBaseTool

  • Description: Get expression data for a C. elegans gene from WormBase. Returns tissues where the gene is expressed, developmental stages, subcellular localization, and expression clusters. Expression data is curated from GFP reporters, antibody staining, RNA in situ, and microarray experiments. Example: WBGene00006763 (unc-26) is expressed in 38 tissues including neurons, pharynx, and body wall muscle.

Parameters:

  • gene_id (string) (required) WormBase gene identifier. Examples: ‘WBGene00006763’ (unc-26), ‘WBGene00000898’ (daf-2).

Example Usage:

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

WormBase_get_gene (Type: WormBaseTool)

Get detailed gene overview from WormBase for C. elegans (nematode worm) by WormBase gene ID. Retu…

WormBase_get_gene tool specification

Tool Information:

  • Name: WormBase_get_gene

  • Type: WormBaseTool

  • Description: Get detailed gene overview from WormBase for C. elegans (nematode worm) by WormBase gene ID. Returns gene name, sequence name, species, description, gene type, and status. C. elegans is one of the most important model organisms for genetics, neuroscience, and developmental biology. Example: WBGene00006763 returns unc-26 (synaptojanin, a polyphosphoinositide phosphatase required for synaptic vesicle recycling).

Parameters:

  • gene_id (string) (required) WormBase gene identifier (WBGene format). Examples: ‘WBGene00006763’ (unc-26), ‘WBGene00006789’ (unc-52), ‘WBGene00000898’ (daf-2).

Example Usage:

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

WormBase_get_human_diseases (Type: WormBaseTool)

Get human disease models (Disease Ontology / DOID) for a C. elegans gene from WormBase, inferred …

WormBase_get_human_diseases tool specification

Tool Information:

  • Name: WormBase_get_human_diseases

  • Type: WormBaseTool

  • Description: Get human disease models (Disease Ontology / DOID) for a C. elegans gene from WormBase, inferred by orthology to human disease genes. Accepts a WBGene ID or gene name. Example: WBGene00006818 (unc-86) is a potential model for DOID:0110546 ‘autosomal dominant nonsyndromic deafness 15’, inferred by orthology to human HGNC:9220.

Parameters:

  • gene_id (string) (required) WBGene identifier or gene name. Examples: ‘WBGene00006818’, ‘unc-86’.

Example Usage:

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

WormBase_get_interactions (Type: WormBaseTool)

Get physical and genetic interactions for a C. elegans gene from WormBase, split into physical an…

WormBase_get_interactions tool specification

Tool Information:

  • Name: WormBase_get_interactions

  • Type: WormBaseTool

  • Description: Get physical and genetic interactions for a C. elegans gene from WormBase, split into physical and genetic lists with interactor names, IDs, interaction type, and citation. Accepts a WBGene ID or gene name. Example: WBGene00006818 (unc-86) has a physical interactor die-1 (WBGene00000995) and a genetic interactor ttx-3 (WBGene00006654).

Parameters:

  • gene_id (string) (required) WBGene identifier or gene name. Examples: ‘WBGene00006818’, ‘unc-86’.

Example Usage:

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

WormBase_get_orthologs (Type: WormBaseTool)

Get orthologs and homologs of a C. elegans gene across species from WormBase (Inparanoid/EnsEMBL-…

WormBase_get_orthologs tool specification

Tool Information:

  • Name: WormBase_get_orthologs

  • Type: WormBaseTool

  • Description: Get orthologs and homologs of a C. elegans gene across species from WormBase (Inparanoid/EnsEMBL-Compara/OrthoFinder etc.), plus nematode orthologs and within-worm paralogs. Accepts a WBGene ID or gene name (auto-resolved). Example: WBGene00006818 (unc-86) returns cross-species orthologs like zebrafish pou4f4 and nematode orthologs like CSP40.g8217 (c_tribulationis).

Parameters:

  • gene_id (string) (required) WBGene identifier or gene name. Examples: ‘WBGene00006818’, ‘unc-86’.

Example Usage:

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

WormBase_get_phenotypes (Type: WormBaseTool)

Get phenotype annotations for a C. elegans gene from WormBase. Returns observed phenotypes (from …

WormBase_get_phenotypes tool specification

Tool Information:

  • Name: WormBase_get_phenotypes

  • Type: WormBaseTool

  • Description: Get phenotype annotations for a C. elegans gene from WormBase. Returns observed phenotypes (from RNAi, mutation, transgene experiments), phenotypes not observed, and total counts. Phenotype data uses the WormBase Phenotype Ontology (WPO). Example: WBGene00006763 (unc-26) has 125+ observed phenotypes including locomotion defects, synaptic vesicle recycling abnormalities, and pharyngeal pumping defects.

Parameters:

  • gene_id (string) (required) WormBase gene identifier. Examples: ‘WBGene00006763’ (unc-26), ‘WBGene00000898’ (daf-2).

Example Usage:

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