Go Api Tools

Configuration File: go_api_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

GOAPI_get_gene_functions (Type: GOAPITool)

Get Gene Ontology (GO) annotations for a specific gene, showing its known biological processes, m…

GOAPI_get_gene_functions tool specification

Tool Information:

  • Name: GOAPI_get_gene_functions

  • Type: GOAPITool

  • Description: Get Gene Ontology (GO) annotations for a specific gene, showing its known biological processes, molecular functions, and cellular components. Returns GO terms with evidence types (IDA=direct assay, IMP=mutant phenotype, ISS=sequence similarity, etc.) and literature references. Input is a gene CURIE identifier. Example: HGNC:11998 (TP53) returns annotations like ‘apoptotic process’, ‘DNA binding’, ‘nucleus’.

Parameters:

  • gene_id (string) (required) Gene identifier as a CURIE. Examples: ‘HGNC:11998’ (TP53), ‘UniProtKB:P04637’ (p53 protein), ‘HGNC:1100’ (BRCA1), ‘MGI:MGI:98834’ (Trp53 mouse). For human genes, use HGNC prefix.

  • rows (integer) (optional) Maximum number of annotations to return (default: 20, max: 100).

  • aspect (string) (optional) Filter by GO aspect: ‘P’ (Biological Process), ‘F’ (Molecular Function), ‘C’ (Cellular Component). Default: all aspects.

Example Usage:

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

GOAPI_get_genes_by_function (Type: GOAPITool)

Get genes annotated with a specific Gene Ontology (GO) term. Find all genes/proteins that have be…

GOAPI_get_genes_by_function tool specification

Tool Information:

  • Name: GOAPI_get_genes_by_function

  • Type: GOAPITool

  • Description: Get genes annotated with a specific Gene Ontology (GO) term. Find all genes/proteins that have been experimentally or computationally associated with a biological process, molecular function, or cellular component. Optionally filter by taxon. Example: GO:0006915 (apoptotic process) returns genes like TP53, BAX, BCL2 that function in apoptosis.

Parameters:

  • go_id (string) (required) Gene Ontology term ID. Examples: ‘GO:0006915’ (apoptotic process), ‘GO:0003677’ (DNA binding), ‘GO:0005634’ (nucleus).

  • rows (integer) (optional) Maximum number of gene annotations to return (default: 20, max: 100).

  • taxon (string) (optional) Filter by taxon. Format: NCBITaxon:ID. Examples: ‘NCBITaxon:9606’ (human), ‘NCBITaxon:10090’ (mouse), ‘NCBITaxon:7227’ (Drosophila).

Example Usage:

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

GOAPI_get_term (Type: GOAPITool)

Get detailed information about a Gene Ontology (GO) term by its GO ID. Returns the term label, fu…

GOAPI_get_term tool specification

Tool Information:

  • Name: GOAPI_get_term

  • Type: GOAPITool

  • Description: Get detailed information about a Gene Ontology (GO) term by its GO ID. Returns the term label, full definition, synonyms, cross-references, and alternative IDs. GO terms describe gene product attributes across three domains: Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). Example: GO:0006915 returns ‘apoptotic process’ with its definition and related terms.

Parameters:

  • go_id (string) (required) Gene Ontology term ID. Format: GO:NNNNNNN. Examples: ‘GO:0006915’ (apoptotic process), ‘GO:0008285’ (negative regulation of cell population proliferation), ‘GO:0005634’ (nucleus), ‘GO:0003677’ (DNA binding).

Example Usage:

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