Combine biomarkerkg (BiomarkerKB KG) into biomarker (BiomarkerKB)#657
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The registry had two very similarly named resources: `biomarker` (BiomarkerKB, the knowledgebase) and `biomarkerkg` (BiomarkerKB KG, its graph representation). Per maintainer decision, combine them into a single entry to avoid confusion. - biomarker.md: absorb the BKG products (explorer, node/edge datasets, OKN/FRINK SPARQL + TPF endpoints), renamed biomarkerkg.* -> biomarker.bkg.* (endpoints as biomarker.sparql / biomarker.tpf to match the FRINK sync output). Merge in the MaayanLab/Jeet Vora contacts and the okn collection, and note the KG in the description. Foreign UBKG products left as-is. - biomarkerkg.md: reduce to a deprecated stub (activity_status: inactive, use_instead: biomarker); remove its 14 product companion files. - Rename biomarkerkg.* -> biomarker.bkg.* and source: biomarkerkg -> biomarker in the cross-listed products under obci, doid, dbsnp, glygen, pubchem, and uberon. - sync_frink.py: alias FRINK shortname "biomarkerkg" -> "biomarker" so the sync updates the canonical page (e.g. endpoint URLs) instead of recreating a biomarkerkg directory, and preserve the canonical resource's identity fields when merging an aliased entry. Add regression tests. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Combines the two near-identically-named resources into a single entry, per the decision to merge rather than disambiguate. Supersedes the closed disambiguation PRs #655 and #656.
biomarker(BiomarkerKB, the knowledgebase) survives as the single active entry and absorbsbiomarkerkg(BiomarkerKB KG, the graph representation).biomarker(surviving entry)biomarkerkg.*→biomarker.bkg.*:biomarker.bkg.explorer(BKG Explorer),biomarker.bkg.nodes.*/biomarker.bkg.edges.*(6 + 5 dataset files)biomarker.sparqlandbiomarker.tpf(see sync note below)okncollection; notes the BKG in the descriptionbiomarkerkg(deprecated stub)activity_status: inactive,use_instead: biomarker, description explains the mergeCross-listed source resources
The BKG node/edge products are also cross-listed under their ontology sources. Renamed
biomarkerkg.*→biomarker.bkg.*andsource: biomarkerkg→source: biomarkerin: obci, doid, dbsnp, glygen, pubchem, uberon. Nobiomarkerkg.*product references remain outside generated build artifacts.FRINK sync (so it won't recreate
biomarkerkg)util/sync_frink.py:biomarkerkg→biomarkerinSHORTNAME_ALIASES, so a FRINK sync updates thebiomarkerpage (e.g. its SPARQL/TPF endpoint URLs) instead of recreating abiomarkerkgdirectory.merge_resource_metadatanow takespreserve_identity: for an aliased entry it will not overwrite the canonical resource's name/description/homepage/status, but still merges products/contacts/collection. The endpoint products are named to match the sync's generated IDs (biomarker.sparql/biomarker.tpf) so they update in place — verified idempotent (a no-op sync when nothing upstream changed).tests/test_frink_sync.py); all 6 pass.All eight changed resource files validate clean. (The one failing
test_integritycase — publication identifiers in agro/sepio/unii — pre-exists onmainand is unrelated.)🤖 Generated with Claude Code