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Knowledge bases

A knowledge base (KB) is a curated list of concepts — terms, ontology entries, named entities — that annotation layers can reference. Instead of annotators typing free-text concept names (with all the typos and variants that brings), a project's typed feature layers point at a KB and annotators pick from it.

Where it lives​

Organization → Resources → Knowledge bases (/organization/resources/knowledge), one of the four Resources sections (Templates, Consent, Labels, Knowledge bases). Reachable by Managers and above (Owner / Admin / Manager).

The page lists the organisation's knowledge bases, ten to a page, each with its kind, entry count and language, its ID pill (kb=2) and the actions Open, Edit and Delete. New knowledge base in the title row opens the create dialog; a new one opens at once. Open shows the knowledge base's entries in a dialog.

Kinds​

KindMeaning
Curated (managed here)Entries are created and edited on the platform — the common case
Formal ontologyA structured ontology (e.g. GO-style identifiers) maintained here
External endpointConcepts resolve against an external service; set its Endpoint URL
WikidataA Wikidata subset; optionally point Endpoint URL at a mirror

Managing entries​

Open a knowledge base to work with its entries in a dialog. Its first line states its kind, entry count, language, ID and endpoint, with Import and Add entry beside it.

  • Add entry — external ID (e.g. GO:0006915), label, optional description and comma-separated aliases, in a small dialog over the open knowledge base.
  • Import — paste or upload TSV/CSV with columns external_id, label, optional description, optional aliases (pipe- or semicolon-separated). A header row is recognised; the dialog says how many rows it read before you import.
  • Find an entry filters the table by ID, label, alias or description; each row has Edit and Delete.

Entries are paginated (10 per page by default).

Referencing a KB from a labeling config​

Every KB shows an ID pill (e.g. kb=2) next to its name. Use that ID in the labeling config's KB reference attribute (kb=) on typed feature layers (concept_kb_ref) so spans, relations, or documents can be tagged with concepts from the list. See typed feature layers for the layer side of the wiring (the <KBRef> control tag).

Deleting​

Deleting a KB removes all its entries and cannot be undone; projects that referenced it will show unresolved concept references until re-pointed.