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Make sure SSSOM-derived xrefs use correct prefixes.
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Most of the prefixes used by the taxon-specific life stage ontologies
(SSLSO) are not intrinsically known by ROBOT (prefixes such as BtauDv,
GgalDv, PpanDv, etc.).

As a result, when the mappings from SSLSO are transformed into
cross-references for injection into the ontology (when we create the
`mappings.owl` component), the SSLSO term IDs are shortened using the
only suitable prefix that ROBOT knows about, the `obo:` prefix.

This means that a mapping to, say,
<http://purl.obolibrary.org/obo/BtauDv_0000078> gets turned into a
cross-reference to `obo:BtauDv_0000078` -- which is, strictly speaking,
correct, but _not_ the format most people would expect for OBO-style
cross-references (which would be BtauDv:0000078).

The fix is simply to make sure the prefixes are correctly declared.
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gouttegd committed Jan 22, 2025
1 parent 9503925 commit ed81eb0
Showing 1 changed file with 23 additions and 0 deletions.
23 changes: 23 additions & 0 deletions src/scripts/mappings-to-xrefs.rules
Original file line number Diff line number Diff line change
@@ -1,6 +1,29 @@
prefix UBERON: <http://purl.obolibrary.org/obo/UBERON_>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
prefix MESH: <http://id.nlm.nih.gov/mesh/>
prefix AcarDv: <http://purl.obolibrary.org/obo/AcarDv_>
prefix BtauDv: <http://purl.obolibrary.org/obo/BtauDv_>
prefix CfamDv: <http://purl.obolibrary.org/obo/CfamDv_>
prefix ChirDv: <http://purl.obolibrary.org/obo/ChirDv_>
prefix CporDv: <http://purl.obolibrary.org/obo/CporDv_>
prefix DpseDv: <http://purl.obolibrary.org/obo/DpseDv_>
prefix DsimDv: <http://purl.obolibrary.org/obo/DsimDv_>
prefix EcabDv: <http://purl.obolibrary.org/obo/EcabDv_>
prefix FcatDv: <http://purl.obolibrary.org/obo/FcatDv_>
prefix GgalDv: <http://purl.obolibrary.org/obo/GgalDv_>
prefix GgorDv: <http://purl.obolibrary.org/obo/GgorDv_>
prefix HsapDv: <http://purl.obolibrary.org/obo/HsapDv_>
prefix MdomDv: <http://purl.obolibrary.org/obo/MdomDv_>
prefix MmulDv: <http://purl.obolibrary.org/obo/MmulDv_>
prefix MmusDv: <http://purl.obolibrary.org/obo/MmusDv_>
prefix OanaDv: <http://purl.obolibrary.org/obo/OanaDv_>
prefix OariDv: <http://purl.obolibrary.org/obo/OariDv_>
prefix OcunDv: <http://purl.obolibrary.org/obo/OcunDv_>
prefix PpanDv: <http://purl.obolibrary.org/obo/PpanDv_>
prefix PtroDv: <http://purl.obolibrary.org/obo/PtroDv_>
prefix RnorDv: <http://purl.obolibrary.org/obo/RnorDv_>
prefix SsalDv: <http://purl.obolibrary.org/obo/SsalDv_>
prefix SscrDv: <http://purl.obolibrary.org/obo/SscrDv_>

# Make sure UBERON classes, and only UBERON classes, are on the object side
subject==UBERON:* -> invert();
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