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Vocabularies & Ontologies

Many fields in LabID — organism, library type, imaging method … — are filled from controlled lists rather than free text. Each list is a vocabulary category (or CVCategory), and the values in it are vocabulary terms (or CVTerm). This keeps data consistent and searchable across the whole instance. You can explore available CVCategory & CVTerm using the corresponding sections in the Vocabularies menu.

A vocabulary term can also be linked to one or more official ontology term(s) (EFO, Cell Ontology, CHEBI, NCBI Taxon, ENA sample attributes, …), pulled from the EBI Ontology Lookup Service. Note that a unique mapping to a given ontology can be defined i.e. a CVTerm can be mapped to several ontologies.

Why it matters:

  • Data quality — one agreed spelling, plus mapping to ontological term ids that do not drift when a term label is corrected.
  • Ready for submission & exchange — terms mapped to ENA / EFO / other ontologies are directly reusable downstream (e.g. ENA submission) and when sharing with other platforms. When mapped to several ontologies, a term can be "translated" to the ontology of choice at export time.
  • Works the same everywhere — sequencing, imaging, chemicals, organisms all use the one mechanism.

What you can do as a user

  • Pick values from the drop-downs as usual
  • Discover available CV terms & categories, imported ontologies and terms, and their mappings using the Vocabularies menu
  • Where a term is linked to an ontology, you see its identifier (e.g. EFO:0009901) next to the label, and a link out to the source ontology.
Vocabulary term with linked ontology term
Vocabulary term with link to ontology term from the EFO ontology. Here both the CVTerm and the ontology term have the same name.

Need a value that is not in the list? Need to define a new mapping between CVTerm and ontologies? Ask your LabID admin — importing ontology terms and linking them to vocabulary terms requires admin credentials.

Self-service term import is planned

Letting users add a missing term straight from an approved ontology (per category, when an admin allows it) is on the roadmap but not available yet. For now, all imports and links go through an administrator.

Managing it (admins)

Creating ontologies, importing them from OLS, pulling in ontology terms and linking vocabulary terms to them — individually or in batches — is done from the Admin UI. See: