Gene Ontology Tools

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

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

Available Tools

GO_get_annotations_for_gene (Type: GeneOntologyTool)

Finds all GO annotations for a specific gene/protein using GOlr search.

GO_get_annotations_for_gene tool specification

Tool Information:

  • Name: GO_get_annotations_for_gene

  • Type: GeneOntologyTool

  • Description: Finds all GO annotations for a specific gene/protein using GOlr search.

Parameters:

  • gene_id (string) (required) A gene identifier such as gene symbol (e.g., ‘TP53’) or database ID.

Example Usage:

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

GO_get_genes_for_term (Type: GeneOntologyTool)

Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.

GO_get_genes_for_term tool specification

Tool Information:

  • Name: GO_get_genes_for_term

  • Type: GeneOntologyTool

  • Description: Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.

Parameters:

  • id (string) (required) The standard GO term ID, e.g., ‘GO:0006915’.

  • taxon (string) (optional) Optional species filter using a NCBI taxon ID. For example, Human is ‘NCBITaxon:9606’, and Mouse is ‘NCBITaxon:10090’.

  • rows (integer) (optional) The number of genes to return. Default is 100.

Example Usage:

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

GO_get_term_by_id (Type: GeneOntologyTool)

Retrieves basic GO term information by ID using GOlr search.

GO_get_term_by_id tool specification

Tool Information:

  • Name: GO_get_term_by_id

  • Type: GeneOntologyTool

  • Description: Retrieves basic GO term information by ID using GOlr search.

Parameters:

  • id (string) (required) The standard GO term ID, e.g., ‘GO:0006915’ for apoptotic process.

Example Usage:

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

GO_get_term_details (Type: GeneOntologyTool)

Retrieves detailed information for a specific GO ID using the Biolink API, including definition, …

GO_get_term_details tool specification

Tool Information:

  • Name: GO_get_term_details

  • Type: GeneOntologyTool

  • Description: Retrieves detailed information for a specific GO ID using the Biolink API, including definition, synonyms, and annotations.

Parameters:

  • id (string) (required) The standard GO term ID, e.g., ‘GO:0006915’ for apoptotic process.

Example Usage:

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

GO_search_terms (Type: GeneOntologyTool)

Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms…

GO_search_terms tool specification

Tool Information:

  • Name: GO_search_terms

  • Type: GeneOntologyTool

  • Description: Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms and related biological entities.

Parameters:

  • query (string) (required) The keyword to search for, e.g., ‘apoptosis’ or ‘kinase activity’.

Example Usage:

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