Skip to content

Vocabulary Management

LabID controls the values users can pick for many properties and annotations (organism, library type, imaging method, …). This is handled by two complementary building blocks:

  • Controlled Vocabulary — the local lists maintained inside your instance (with some shipping defaults). A CV Category groups a set of CV Terms, and a property or annotation is mapped to a category to obtain its drop-down of allowed values.
  • Ontologies — a bridge between those local terms and official ontology terms (EFO, Cell Ontology, CHEBI, ENA sample attributes, …), imported from the EBI Ontology Lookup Service (OLS) or defined manually.

  • Controlled Vocabulary

    Create and maintain CV Categories and CV Terms, through the Admin UI or in bulk from the command line.

  • Ontologies

    Import ontologies from EBI OLS (or create them from scratch), pull in ontology terms, and link your vocabulary terms to them — individually or in batches.

How the two fit together

 Item property  ──▶ [mapped to] ──▶ CV Category ──▶ [contains]  ──▶ CV Term
      or 
 Annotation Type                      │                          │
                                (many-to-many)            (many-to-many)
                                      │                          │
                                      ▼                          ▼
                                  Ontology     ──▶ [contains]  ──▶  Ontology Term
  • A CV Term can be linked to one or more Ontology Terms (many-to-many). This replaces the old single free-text dbxref field: a term can now carry an EFO id and an ENA id, for example.
  • A CV Category can list one or more Ontologies as allowed sources (many-to-many). Term search and import on that category are restricted to those ontologies.
  • Every imported (or manually created) ontology has one default CV Category. Whenever an ontology term is imported, a matching CV Term is created in that default category, so the value is immediately usable in drop-downs without any extra step.

Where to find it in the UI

Everything below lives under the Vocabularies menu of the UI: Vocabulary Categories, Terms, Ontologies and Ontology Terms.

What it buys you

  • Better data quality — values are spelled once, consistently, and carry a stable identifier instead of a name that can drift.
  • Interoperability — terms mapped to EFO / ENA / Cell Ontology / CHEBI are ready for downstream submission (e.g. ENA) and for exchange with other platforms.
  • Multi-omics & imaging ready — the same mechanism serves sequencing library attributes, imaging methods, cell lines, chemicals, organisms, …