Ontologies

The ontology module connects your local controlled vocabulary to official ontology terms — from the EBI Ontology Lookup Service (OLS) or defined by hand for sources that are not on OLS (such as the ENA sample attributes).

Linking a CV Term to an Ontology Term gives it a stable identifier (e.g. EFO:0009901, CLO_0037280, CHEBI:27958) on top of its label. That identifier is what makes the data reusable: ready for ENA submission, comparable across omics, and unambiguous when a label is later corrected.

See also

The Vocabulary Management overview explains how CV Category, CV Term, Ontology and Ontology Term relate to each other.

Concepts

Object	What it is
Ontology	A source (EFO, Cell Ontology, ENA, …). Carries a code, homepage, OLS URL and version.
Ontology Term	A single concept from an ontology, with its term id and label. Stored in LabID only once it is linked to a vocabulary term.
Default category	Every ontology has exactly one. A matching CV Term is created there whenever one of its terms is imported.
Allowed sources	A CV Category can list several ontologies. Term search and import on that category are limited to those ontologies.

CV Term ↔ Ontology Term and CV Category ↔ Ontology are both many-to-many relationships.

Creating an ontology UI · Admin only

Only administrators can create or edit ontologies. Go to Vocabularies > Ontologies and use the New Ontology button.

The Vocabularies > Ontologies list. Imported ontologies keep an imported marker.

Import from EBI OLS

• New Ontology › Import from OLS. Search the OLS catalogue (e.g. for key ad). Each row shows its id, description and term count. Pick an ontology from the results by clicking on Import.

Searching the OLS catalogue.

• Next, choose the default CV Category under Assign Categories: link to an existing category or create a new one (named after the ontology code). This becomes the ontology's default category.
• Click Import to finalize the import.

Only the ontology metadata is imported. Individual terms are stored later, when you link them to vocabulary terms.

Importing an ontology does not import its terms

An ontology can hold tens of thousands of terms. The import only brings in the ontology itself. Terms are added on demand — one by one from Search & Import from OLS, or in bulk from Batch Link Terms.

Create from scratch

New Ontology › New Ontology creates an ontology manually. Use it for sources that are not on OLS — for instance the vocabularies used by the ENA. Provide a name, a code, a description and (optionally) a homepage, and assign the default category as above. Its terms are then added manually from Vocabularies > Ontology Terms > New Ontology Term.

The default shipping European Nucleotide Archive ontology was created from scratch.

Linking a CV category to more ontologies

The category page is the starting point.

A CV category connected to the imported "Addiction Ontology".

Use Manage Ontologies button to add or remove ontologies from the ontology sources.

Editing the ontology sources.

Importing ontology terms

Search & import from OLS UI · Admin only

Who can do this

Searching the EBI OLS is open to every authenticated user, but importing a term (which also creates a vocabulary term) is currently reserved to administrators. Regular users request new terms from an admin.

From Vocabularies > Ontology Terms, use New Ontology Term › Search & Import from OLS.

The Ontology Terms list, with the import menu open.

Type a query, optionally restrict it to one ontology and tick Exact match. Results show the label, ontology, term id and whether the term is obsolete. Terms already present in LabID are flagged, along with the vocabulary terms and categories that use them.

Pressing Import on a row:

• stores the Ontology Term, and
• creates a matching CV Term in the ontology's default category, with its dbxref_id set to the OLS short id (e.g. CHEBI:27958).

You stay on the search page so you can import several terms in a row.

Searching OLS terms, scoped to Cell Ontology.

Correct attribution

OLS also returns terms an ontology merely re-uses. LabID only lets you import a term into the ontology that actually defines it, so a scoped search may return fewer results than the raw OLS website — this is expected.

Ownership of imported terms

Ontology terms, and the vocabulary terms created alongside them, are always public. Their ownership follows the container (the Ontology or the CV Category); the admin who ran the import is recorded as the creator.

Letting users import terms — planned

Allowing regular users to add a missing term straight from an approved ontology — opt-in per CV Category, with the OLS search restricted to that category's linked ontologies — is on the roadmap but not available yet. Until then, term import stays with administrators.

Linking vocabulary terms to ontology terms UI · Admin only

Linking existing vocabulary terms to ontology terms is reserved to administrators.

Single link

From a CV Term page, Link to Ontology lets you search the category's allowed ontologies and link (or unlink) an ontology term. A vocabulary term can hold one link per ontology, but links to several different ontologies.

A local CV Term cocaine addict not connected to any ontological term. One allowed ontology source is defined: Addiction Ontology

In the right panel, click the Link this term to Ontology button, use the search bar to look for e.g. cocai.

Searching terms in the source ontology.

Click the ontology term to link it to the term (here we chose cocaine user).

The local term cocaine addict is now linked to the ontology term.

Batch link

Batch Link Terms processes a whole category at once. Start it from:

• an Ontology page — covers every category linked to that ontology, or
• a CV Category page — scoped to that category; you first pick which of its linked ontologies to match against.

From a category page, batch linking runs against one chosen ontology.

In the modal, LabID searches OLS for every term in the category and proposes a match:

• The table columns are Term Name, Term Category, Linked Ontology Term and Suggested OLS Match.
• Select All Matched / Deselect All to pick the rows to link.
• Change / Search on a row to adjust the proposed match. Editing the search text marks the row with a Modified tag.
• Add New Term finds an OLS term and adds it as a brand-new CV Term (tagged New) linked to that ontology term.
• Link N Term(s) commits the selection. Already-linked terms can be hidden or shown.

Batch linking the celltypes and D categories against the Cell Line Ontology.

When no match is found, you can still adapt the search term live, in which case a Modified tag is visible:

Refining a row's search — the row is tagged Modified.

The Add New Term button at the top right allows to find an ontology term and add it immediately as a new CVTerm linked to this ontology term

A term added through Add New Term is tagged New.

The result is visible on the Ontology Terms panel of the ontology, and in the Ontology column / links on each vocabulary term.

The Ontology Terms panel, with the vocabulary terms linked to each ontology term.

Access rules at a glance

Action	Who
Search OLS terms	any authenticated user
Create / edit / delete an Ontology	administrators
Manage a category's ontology sources	administrators
Import an ontology term (also creates a CV Term)	administrators
Link an existing CV Term to an ontology term (single or batch)	administrators
Add a missing term from an approved ontology, per category	planned — not available yet

Imported ontology terms and the vocabulary terms created alongside them are always public. Ownership follows the container (the Ontology or the CV Category), not the person who ran the import; that person is still recorded as the creator.

Keeping terms up to date

A term's description and its obsolete flag are captured at import time. There is no automatic re-synchronisation with OLS yet — re-import a term to refresh it.