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 annotations for a specific gene with explicit start/rows pagination. The GO API…

GOAPI_get_gene_functions tool specification

Tool Information:

  • Name: GOAPI_get_gene_functions

  • Type: GOAPITool

  • Description: Get Gene Ontology annotations for a specific gene with explicit start/rows pagination. The GO API omits a total count, so ToolUniverse uses one-record look-ahead to report exact has_more and next_start; total_results is populated only on the final page and total_results_exact states whether it is known.

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) Annotations per page (default 20, verified upstream through 1000). ToolUniverse requests one extra association internally to determine has_more.

  • start (integer) (optional) Zero-based association offset. Continue with metadata.next_start while has_more is true.

  • 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 unique genes annotated with a GO term. The upstream /genes route actually returns repeated as…

GOAPI_get_genes_by_function tool specification

Tool Information:

  • Name: GOAPI_get_genes_by_function

  • Type: GOAPITool

  • Description: Get unique genes annotated with a GO term. The upstream /genes route actually returns repeated association rows, so ToolUniverse deduplicates by gene ID, preserves the encountered GO/evidence/provider rows under each gene, and applies offset after deduplication. Metadata reports unique-gene navigation and scan completeness; each gene’s associations_complete flag states whether its nested association list is proven complete.

Parameters:

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

  • rows (integer) (optional) Unique genes per locally deduplicated page (default 20, max 1000).

  • offset (integer) (optional) Zero-based offset after deduplication by gene ID. Continue with metadata.next_offset while has_more is true.

  • max_associations_scanned (integer) (optional) Optional upstream association-row scan budget. Increase and rerun the same offset if metadata.scan_limit_reached is true or complete nested associations are required.

  • 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)