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Ontology Term Lookup

Metaseed provides integrated ontology term lookup using the OLS4 (Ontology Lookup Service) API. This enables users to search and select standardized ontology terms when editing metadata.

Overview

Fields with type: ontology_term automatically get:

  • Autocomplete: Type-ahead suggestions as you type
  • Modal search: Full search interface via Tab key or search button
  • OLS4 integration: Real-time queries to the EBI Ontology Lookup Service
  • Smart display: Selected terms show as "label (ID)" for readability

Field Configuration

Basic Ontology Field

fields:
  - name: organism
    type: ontology_term
    description: Scientific name of the organism

This creates an input that searches across all ontologies in OLS4.

Scoped to Specific Ontologies

Use ontologies to restrict searches to specific ontology IDs:

fields:
  # Single ontology
  - name: organism
    type: ontology_term
    ontologies: ["ncbitaxon"]
    description: Organism from NCBI Taxonomy

  # Multiple ontologies
  - name: trait
    type: ontology_term
    ontologies: ["pato", "to"]
    description: Trait from PATO or Trait Ontology

Common ontology IDs:

ID Ontology
ncbitaxon NCBI Taxonomy (organisms)
pato Phenotype and Trait Ontology
envo Environment Ontology
go Gene Ontology
obi Ontology for Biomedical Investigations
po Plant Ontology
chebi Chemical Entities of Biological Interest
uo Units of Measurement Ontology
co_321 Crop Ontology - Wheat traits
agro Agronomy Ontology
peco Plant Experimental Conditions Ontology

Browse all available ontologies at OLS4 Ontologies. The lowercase ontology ID shown in the URL (e.g., ncbitaxon from /ols4/ontologies/ncbitaxon) is the value to use in the ontologies field.

User Interface

Autocomplete

When typing in an ontology term field:

  1. Start typing (minimum 1 character)
  2. Suggestions appear after 300ms debounce
  3. Use arrow keys to navigate
  4. Press Enter or click to select
  5. Press Escape to dismiss

Each suggestion shows: - Term ID (e.g., PATO:0000001) - Label (e.g., "quality") - Source ontology - Description (truncated)

Display Format

After selection, terms display as "label (ID)" for readability:

  • centimeter (UO:0000015) instead of UO:0000015
  • temperature (PATO:0000146) instead of PATO:0000146

The underlying data stores only the ID for interoperability.

For more detailed browsing:

  1. Press Tab when the input is focused, or
  2. Click the search button (magnifying glass icon)

The modal provides: - Full-text search across term labels and descriptions - Multi-select capability - Chip display of selected terms - Detailed term information

API Endpoint

The lookup uses the /api/ontology/search endpoint:

GET /api/ontology/search?q=temperature&ontology=pato

Parameters: - q (required): Search query - ontology (optional): Ontology ID(s) to filter results (comma-separated)

Response: 

{
  "results": [
    {
      "value": "PATO:0000146",
      "label": "temperature",
      "description": "A physical quality...",
      "ontology": "PATO"
    }
  ]
}

Profile Configuration

Define available ontologies in your profile's ontologies section:

spec_version: "0.4"
name: my-profile
version: "1.0"

ontologies:
  PATO:
    name: Phenotype and Trait Ontology
    uri: http://purl.obolibrary.org/obo/pato.owl
    ols_id: pato
  ENVO:
    name: Environment Ontology
    uri: http://purl.obolibrary.org/obo/envo.owl
    ols_id: envo

entities:
  Sample:
    fields:
      - name: quality
        type: ontology_term
        ontologies: ["pato"]
      - name: environment
        type: ontology_term
        ontologies: ["envo"]

The ols_id field maps to the OLS4 ontology identifier used for API queries.

HTML/CSS Classes

For developers extending the UI:

Class Purpose
lookup-input Enables autocomplete behavior
ontology-lookup-btn Search button that opens modal
autocomplete-dropdown Suggestion dropdown container
ontology-autocomplete Ontology-specific dropdown styling

Data attributes: - data-lookup-type="ontology" - Identifies ontology lookup - data-ontologies="pato,envo" - Scopes to specific ontologies (comma-separated)

Keyboard Shortcuts

Key Action
Tab Open search modal (when no dropdown visible)
Tab Select highlighted item (when dropdown visible)
Enter Select highlighted item
Escape Close dropdown or modal
Arrow Up/Down Navigate suggestions

See Also