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Ontology Filter Fixes

Ontology Prefix Counts (MI/OM showing 0)

Problem: The ontology filter sidebar only showed counts for prefixes with annotation bitmaps (GO, CHEBI, HP). MI and OM terms had no entity annotation bitmaps because most MI terms annotate relations (not entities) and OM terms are used for entity typing, not annotations.

Fix:

  1. Inserted missing ontology terms into entity table:

    • 43,009 terms were missing from entity (only 46,729 existed; 89,738 total in ontology_term).
    • Inserted as entity_type = 'OM:0012:Cv Term' with canonical_identifier_type = 'OM:0204:Cv Term Accession'.
    • Updated sources array to include the ontology prefix.

  2. Fixed bitmap rebuild procedures:

    • rebuild_annotation_term_bitmaps() was referencing the non-existent entity_annotation table.
    • Updated to use entity_relation with relation_category = 'annotation'.
    • Updated rebuild_annotation_term_relation_bitmaps() to use relation_annotation_term joined with entity.

  3. Rebuilt all bitmaps via CALL rebuild_all_bitmaps().

  4. Updated getScopedOntologyPrefixCounts:

    • No scope (explore page): returns total term counts per prefix from ontology_term table.
    • With scope (selection annotation tab): returns scoped annotation counts as before.

Result: MI (1,653) and OM (321) now appear in the explore page filter sidebar with correct counts.

Files changed:

  • omnipath-svelte/src/lib/server/queries/ontology-term.ts

Next Step

Review omnipath_build build process to align ontology term handling — ensure all ontology terms are inserted into entity during build, and that the sources field is populated with the ontology prefix.

We should also connect make connect sources as a foreign key to the resources table, maybe we could use the resource name here as a key? and then in the resources we should have a special kind for ontology resources? so we give ontology sources a different icon/emoji in the ui. i guess we also need input modules for ontologies then, but these can be quite minimalistic since we only need to download and parse obo files, which are very standardized.