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 both GO evidence abbreviations and ECO accessions, qualifiers, and annotation sources. Results are pageable and can be filtered by an exact ECO evidence code. Accepts UniProtKB accessions (e.g., ‘UniProtKB:P04637’ for TP53).

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) Number of annotations per page. Default: 25, max: 100.

  • page (integer) (optional) One-based result page. Use metadata.next_page while metadata.has_more is true.

  • evidence_code ([‘string’, ‘null’]) (optional) Exact Evidence and Conclusion Ontology (ECO) accession filter, such as ‘ECO:0000314’ for direct assay evidence. This is distinct from the returned GO evidence abbreviation such as IDA.

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, GO evidence abbreviations, ECO accessions, and annotation sources. Results are pageable and can be filtered by species or an exact ECO evidence code. Example: GO:0006915 (apoptotic process) returns thousands of 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) Number of annotations per page. Default: 25, max: 100.

  • page (integer) (optional) One-based result page. Use metadata.next_page while metadata.has_more is true.

  • evidence_code ([‘string’, ‘null’]) (optional) Exact Evidence and Conclusion Ontology (ECO) accession filter, such as ‘ECO:0000314’ for direct assay evidence.

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)