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UBERON synonyms containing extended characters #1173
Marking as urgent because this issue is preventing Gene Ontology editors to commit changes using OBO-Edit (we load UBERON along with GO, and we still use OBO-Edit for tasks that can't be performed easily in Protege such as adding taxon constraints). These are the culprits:
4 fatal errors:
The fatal errors are like this - look at the synonyms at the top of this entry:
Melanie (Courtot) confirmed that the error is in the source Uberon:
Seems like someone was editing in UTF-8 and there was an issue with conversion (potentially with OBO edit which AFAIK supports only ASCII)
Could this be fixed asap please?
These synonyms seem to be housed in the Phenoscape ext file (http://sourceforge.net/p/phenoscape/code/HEAD/tree/trunk/vocab/edit/phenoscape-ext.owl), but it looks like this text encoding problem has been there for a long time. They should be fixed though (but would still have accents).
OBO-Edit should support UTF-8, unless something has broken in the last couple of years. There is a setting in Configuration Manager to allow extended characters—I wonder if that would help you in the immediate term.
Problem averted for GO with this fix to the module extraction pipeline: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/Makefile?r1=29572&r2=29750