Planteome Tools#

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

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

Available Tools#

Planteome_get_term (Type: PlanteomeTool)#

Get a single Planteome ontology term by its accession ID (from Planteome_search_terms or Planteom…

Planteome_get_term tool specification

Tool Information:

  • Name: Planteome_get_term

  • Type: PlanteomeTool

  • Description: Get a single Planteome ontology term by its accession ID (from Planteome_search_terms or Planteome_search_annotations results). Example: term_id=’GO:0009555’ returns the full definition of ‘pollen development’.

Parameters:

  • term_id (string) (required) Ontology term accession, e.g. ‘GO:0009555’ or ‘PO:0025281’.

Example Usage:

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

Planteome_search_annotations (Type: PlanteomeTool)#

Search Planteome’s gene-to-ontology-term annotation index by gene id or accession. Resolves a pla…

Planteome_search_annotations tool specification

Tool Information:

  • Name: Planteome_search_annotations

  • Type: PlanteomeTool

  • Description: Search Planteome’s gene-to-ontology-term annotation index by gene id or accession. Resolves a plant gene to every ontology term (GO/PO/TO/crop ontologies) it has been annotated with, across evidence types and source databases. Example: query=’AT4G32150’ (Arabidopsis VAMP711) returns its GO annotations including ‘vesicle-mediated transport’.

Parameters:

  • query (string) (required) Gene id or accession, e.g. ‘AT4G32150’.

  • limit ([‘integer’, ‘null’]) (optional) Max annotations to return, 1-100. Default 20.

Example Usage:

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

Planteome_search_terms (Type: PlanteomeTool)#

Search Planteome (a Global Core Biodata Resource) for plant ontology terms by keyword, across the…

Planteome_search_terms tool specification

Tool Information:

  • Name: Planteome_search_terms

  • Type: PlanteomeTool

  • Description: Search Planteome (a Global Core Biodata Resource) for plant ontology terms by keyword, across the Plant Ontology, Plant Trait Ontology, Plant Stress Ontology, and crop-specific ontologies together. Example: query=’pollen’ returns terms like ‘pollen development’ (GO:0009555) and crop-specific pollen traits. Complements ToolUniverse’s generic GO tools (OLS/QuickGO), which don’t carry plant-specific trait/structure ontologies.

Parameters:

  • query (string) (required) Keyword or phrase, e.g. ‘pollen development’.

  • limit ([‘integer’, ‘null’]) (optional) Max terms to return, 1-100. Default 20.

Example Usage:

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