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Add HOIP and SSBD ontologies to registry - #128
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Adds two RIKEN ontologies (both led by Yuki Yamagata, CC-BY 4.0) to the non-OBO registry: - hoip: Homeostasis Imbalance Process Ontology (COVID-19 infectious courses, cellular senescence). Fetched from BioPortal, which the upstream README names as the distribution point; the GitHub repo only carries a date-stamped zip of the same file. The 2024-04-03 release tags two synonyms with xml:lang="a", which is not a valid language tag and makes rdftab abort, so the build rewrites that tag to "en". - ssbd: SSBD Ontology, bioimaging dataset metadata for the RIKEN SSBD repository. Fetched from GitHub (ssbd_integrated.owl), the primary release; the BioPortal submission is the same graph minus later property-name typo fixes. Its prefixmap also contracts NCBI Gene web IRIs to NCBIGene (alongside the existing identifiers.org base) and JAX mouse strain IRIs to jax. Both were built end-to-end (robot + rdftab + relation-graph) and checked for CURIE contraction and is-a closure with OAK; ontologies.Makefile and prefixes.csv/prefixes_local.csv are regenerated accordingly. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VjkEivqeSxzN18QBsWsU1K
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Summary
Adds two new biomedical ontologies to the semantic-sql ontology registry: the Homeostasis Imbalance Process Ontology (HOIP) and the SSBD Ontology for bioimaging metadata.
Changes
HOIP Ontology: Added download and build rules with XML language tag correction
xml:lang="a"tags (typo for "en") that would cause rdftab to abortSSBD Ontology: Added download and build rules
Build infrastructure: Updated
ontologies.Makefilewith download/build rules following existing patternsRegistry: Added entries to
src/semsql/builder/registry/ontologies.yamlwith descriptions and metadataPrefix mappings: Updated both
prefixes.csvandprefixes_local.csvwith new namespace URIsImplementation Details
The HOIP entry includes a custom
build_commandto work around a data quality issue in the 2024-04-03 release where two synonyms use an invalid BCP 47 language tag. This preprocessing step ensures compatibility with rdftab's RDF parsing.Both ontologies follow the established registry pattern and will be included in the standard build pipeline via the
EXTRA_ONTOLOGIESvariable.