Quickgo Tools

Configuration File: quickgo_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

QuickGO_annotations_by_gene (Type: QuickGOTool)

Search Gene Ontology (GO) annotations for a specific gene product using the EBI QuickGO browser. …

QuickGO_annotations_by_gene tool specification

Tool Information:

  • Name: QuickGO_annotations_by_gene

  • Type: QuickGOTool

  • Description: Search Gene Ontology (GO) annotations for a specific gene product using the EBI QuickGO browser. Returns GO terms annotated to the protein/gene with evidence codes, qualifiers, and annotation sources. Accepts UniProtKB accessions (e.g., ‘UniProtKB:P04637’ for TP53). Provides more detailed annotation data than the standard GO API, including evidence provenance and assigned-by information. Useful for understanding gene function, localization, and biological processes.

Parameters:

  • gene_product_id (string) (required) Gene product identifier, typically a UniProtKB accession. Format: ‘UniProtKB:P04637’ (TP53), ‘UniProtKB:P38398’ (BRCA1), ‘UniProtKB:P00533’ (EGFR).

  • aspect ([‘string’, ‘null’]) (optional) Filter by GO aspect: ‘biological_process’, ‘molecular_function’, or ‘cellular_component’. Default: all aspects.

  • taxon_id ([‘integer’, ‘null’]) (optional) Filter by NCBI taxonomy ID. Example: 9606 (human), 10090 (mouse).

  • limit (integer) (optional) Maximum number of annotations to return. Default: 25, max: 100.

Example Usage:

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

QuickGO_annotations_by_goterm (Type: QuickGOTool)

Search for all gene products annotated with a specific Gene Ontology (GO) term using the EBI Quic…

QuickGO_annotations_by_goterm tool specification

Tool Information:

  • Name: QuickGO_annotations_by_goterm

  • Type: QuickGOTool

  • Description: Search for all gene products annotated with a specific Gene Ontology (GO) term using the EBI QuickGO browser. Returns the proteins/genes associated with the GO term, their evidence codes, and annotation sources. Can be filtered by species (taxon_id). Useful for finding all genes involved in a biological process, molecular function, or cellular component. Example: GO:0006915 (apoptotic process) returns 6800+ human annotations.

Parameters:

  • go_id (string) (required) Gene Ontology term accession. Examples: ‘GO:0006915’ (apoptotic process), ‘GO:0008150’ (biological process), ‘GO:0005634’ (nucleus), ‘GO:0003677’ (DNA binding).

  • taxon_id ([‘integer’, ‘null’]) (optional) Filter by NCBI taxonomy ID. Example: 9606 (human), 10090 (mouse), 7227 (fly).

  • limit (integer) (optional) Maximum number of annotations to return. Default: 25, max: 100.

Example Usage:

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

QuickGO_get_term_children (Type: QuickGOTool)

Get child terms (direct descendants) of a Gene Ontology (GO) term from the EBI QuickGO browser. R…

QuickGO_get_term_children tool specification

Tool Information:

  • Name: QuickGO_get_term_children

  • Type: QuickGOTool

  • Description: Get child terms (direct descendants) of a Gene Ontology (GO) term from the EBI QuickGO browser. Returns child term IDs, names, relationship type (is_a, part_of, regulates), and whether they have further children. Useful for navigating the GO hierarchy and finding more specific terms. Example: GO:0006915 (apoptotic process) has 29 children including ‘intrinsic apoptotic signaling pathway’ and ‘extrinsic apoptotic signaling pathway’.

Parameters:

  • go_id (string) (required) Gene Ontology term accession. Examples: ‘GO:0006915’ (apoptotic process), ‘GO:0008150’ (biological process), ‘GO:0005575’ (cellular component).

Example Usage:

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

QuickGO_get_term_detail (Type: QuickGOTool)

Get detailed information about a specific Gene Ontology (GO) term from the EBI QuickGO browser. R…

QuickGO_get_term_detail tool specification

Tool Information:

  • Name: QuickGO_get_term_detail

  • Type: QuickGOTool

  • Description: Get detailed information about a specific Gene Ontology (GO) term from the EBI QuickGO browser. Returns the term name, definition, aspect (biological_process/molecular_function/cellular_component), synonyms, cross-references, and number of child terms. More detailed than the standard GO term lookup, including synonym types and cross-references to other ontologies. Example: GO:0006915 returns ‘apoptotic process’ with its full definition and 29 child terms.

Parameters:

  • go_id (string) (required) Gene Ontology term accession. Examples: ‘GO:0006915’ (apoptotic process), ‘GO:0008150’ (biological process), ‘GO:0005634’ (nucleus), ‘GO:0016020’ (membrane).

Example Usage:

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