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 GO annotations for a specific gene/protein using GOlr search. Returns one row per annotatio…

GO_get_annotations_for_gene tool specification

Tool Information:

  • Name: GO_get_annotations_for_gene

  • Type: GeneOntologyTool

  • Description: Finds GO annotations for a specific gene/protein using GOlr search. Returns one row per annotation, so a gene with several evidence codes for the same GO term appears several times. This returns a PAGE, not the complete set: heavily annotated genes have far more annotations than one page holds (measured: ‘TP53’ matches 1812 annotation rows). metadata reports the exact total_rows, has_more and next_start; continue with start=metadata.next_start while has_more is true. Supply taxon to avoid mixing same-symbol genes from different organisms; omitting it searches all taxa.

Parameters:

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

  • rows (integer) (optional) Maximum number of annotation rows to return per page (1-1000). Default: 100. A heavily annotated gene such as TP53 has 1812 annotation rows; page through them with start/metadata.next_start, or lower rows to keep responses small.

  • taxon (string) (optional) Optional NCBI taxon filter, e.g. ‘NCBITaxon:9606’ for human. Omit to search all organisms.

  • start (integer) (optional) Zero-based annotation-row offset. Use metadata.next_start to retrieve the next page.

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 genes/proteins annotated to a Gene Ontology term, including annotations to its descendant t…

GO_get_genes_for_term tool specification

Tool Information:

  • Name: GO_get_genes_for_term

  • Type: GeneOntologyTool

  • Description: Finds genes/proteins annotated to a Gene Ontology term, including annotations to its descendant terms (is_a/part_of closure), via the GO Solr index. Pagination uses GOlr annotation rows, which are then collapsed to distinct genes on each page; therefore adjacent pages can contain the same gene and the exact total is an annotation-row total, not a distinct-gene total. Supply taxon to restrict to one species – omit it and genes from all species are returned together.

Parameters:

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

  • taxon (string) (optional) Optional species filter using an NCBI taxon ID, e.g. ‘NCBITaxon:9606’ (human) or ‘NCBITaxon:10090’ (mouse). Omit to return genes from every species.

  • rows (integer) (optional) Maximum number of annotation rows to scan. Distinct genes returned may be fewer, since one gene can carry several annotations. Default is 100.

  • start (integer) (optional) Zero-based offset into GOlr annotation rows. Use metadata.next_start to continue.

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 non-obsolete Gene Ontology terms by a keyword or phrase in term labels and synonyms usin…

GO_search_terms tool specification

Tool Information:

  • Name: GO_search_terms

  • Type: GeneOntologyTool

  • Description: Searches non-obsolete Gene Ontology terms by a keyword or phrase in term labels and synonyms using GOlr. Results are relevance-ranked and support exact-count start/rows pagination.

Parameters:

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

  • rows (integer) (optional) Maximum number of matching GO terms to return.

  • start (integer) (optional) Zero-based result offset. Use metadata.next_start to continue.

Example Usage:

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