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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Wikipathways data revealed a bug in the Merger #222

Closed IgorRodchenkov closed 9 years ago

IgorRodchenkov commented 9 years ago

In original (and thus in the normalized) Wikipathways data, there are e.g. different type EntityReference objects (Dna/Rna/ProteinReference) in multiple files that have the same Identifiers.org based URI. And cPath2 Merger did not replace such URIs with new ones (to use PC2 xml:base), which causes then various range violation errors (mostly about SPE.entityReference property) during the merge of these multiple models into a single target model...

PS: Looks, we should only use the Identifiers.org URIs for valid UnificationXrefs (e.g., UniProt, ChEBI) and PublicationXrefs (PubMed), but not for any EntityReference nor ControlledVocabulary types...

IgorRodchenkov commented 9 years ago

Done (via fixing in the Merger). Wikipathways authors will probably fix the data export (shared URIs) by the next release.