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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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PC2 v7: some Xrefs lack db or id property value(s). #216

Closed IgorRodchenkov closed 9 years ago

IgorRodchenkov commented 9 years ago

Reported (emailed) by Rudolf Pillich (UCSD, NDEx).

  1. Pathway Commons.7.Database of Interacting Proteins.BIOPAX.owl: this reference has no id attribute in it. TAXONOMY/bp:db /bp:UnificationXref
  2. Pathway Commons.7.PhosphoSitePlus.BIOPAX.owl: this segment has no id attribute, it has no db attribute either. REPLACED http://www.phosphosite.org/phosphosite.owl#xref_32670100/bp:comment /bp:UnificationXref
  3. Pathway Commons.7.PANTHER Pathway.BIOPAX.owl: this XREF segment is missing db and id attributes. REPLACED TRANSLATION/bp:comment /bp:RelationshipXref

TODO: 1. can be fixed in the psimi-converter (Paxtools); 2. and 3. and alike - in cPath2, after merge stage or in each provider-specific "cleaner" - simply iterate over all Xrefs and remove bad ones (that have either no 'id' or 'db' or both).