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noctua entity ontology
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NEO script fails if case is different for "name" (column 3 in gaf) #18

Open elserj opened 7 years ago

elserj commented 7 years ago

Didn't mean to open this without comment. Oops.

Anyway, I have 2 gafs that have the following for the first 3 columns of the gaf file that I'm trying to use neo to create a combined owl file to load in noctua: GR_gene GR:0101186 Zep1 GR_gene GR:0101186 ZEP1

The only difference is the case. If I manually change one of them, make successfully completes.

The error I get on a failure:

Exception in thread "main" org.semanticweb.owlapi.model.OWLOntologyStorageException: org.obolibrary.oboformat.model.FrameStructureException: multiple name tags not allowed. in frame:Frame(http://purl.obolibrary.org/obo/GR_gene_GR%3A0101186 id( http://purl.obolibrary.org/obo/GR_gene_GR%3A0101186{}[])relationship( in_taxon NCBITaxon:4530{}[])name( ZEP1 Oryz{}[])synonym( ZEP1 BROAD{}[NCBITaxon:4530 ])synonym( Os04g0448900 Oryz EXACT{}[])synonym( micro RNA 806a Oryz EXACT{}[])synonym( Zeaxanthin epoxidase 1 Oryz EXACT{}[])synonym( Zep1 BROAD{}[NCBITaxon:4530 ])name( Zep1 Oryz{}[])is_a( CHEBI:23367{}[]))
        at org.coode.owlapi.oboformat.OBOFormatRenderer.render(OBOFormatRenderer.java:79)
        at org.coode.owlapi.oboformat.OBOFormatStorer.storeOntology(OBOFormatStorer.java:74)
        at org.semanticweb.owlapi.util.AbstractOWLOntologyStorer.storeOntology(AbstractOWLOntologyStorer.java:211)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1040)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1021)
        at owltools.io.ParserWrapper.saveOWL(ParserWrapper.java:265)
        at owltools.io.ParserWrapper.saveOWL(ParserWrapper.java:213)
        at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:2922)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
        at owltools.cli.CommandRunner.run(CommandRunner.java:237)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
        at owltools.cli.CommandRunner.run(CommandRunner.java:237)
        at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)
Caused by: org.obolibrary.oboformat.model.FrameStructureException: multiple name tags not allowed. in frame:Frame(http://purl.obolibrary.org/obo/GR_gene_GR%3A0101186 id( http://purl.obolibrary.org/obo/GR_gene_GR%3A0101186{}[])relationship( in_taxon NCBITaxon:4530{}[])name( ZEP1 Oryz{}[])synonym( ZEP1 BROAD{}[NCBITaxon:4530 ])synonym( Os04g0448900 Oryz EXACT{}[])synonym( micro RNA 806a Oryz EXACT{}[])synonym( Zeaxanthin epoxidase 1 Oryz EXACT{}[])synonym( Zep1 BROAD{}[NCBITaxon:4530 ])name( Zep1 Oryz{}[])is_a( CHEBI:23367{}[]))
        at org.obolibrary.oboformat.model.Frame.checkMaxOneCardinality(Frame.java:383)
        at org.obolibrary.oboformat.model.Frame.check(Frame.java:357)
        at org.obolibrary.oboformat.model.OBODoc.check(OBODoc.java:344)
        at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:205)
        at org.coode.owlapi.oboformat.OBOFormatRenderer.render(OBOFormatRenderer.java:76)
        ... 12 more
Makefile:28: recipe for target 'neo.obo' failed

Let me know if I need to supply any more info.