caro.owl is not xml/rdf

[vjcitn]

how can it be translated to a more familiar form of owl?

[cmungall]

See also: OBOFoundry/OBOFoundry.github.io#360

You can use robot convert -i caro.owl -o caro-fixed.owl for now https://github.com/ontodev/robot

[vjcitn]

Thanks for checking this.

robot is not completely happy, and then when python pronto conversion to obo is attempted, we have no success. here is the robot complaint

%vjcair> robot convert -i caro.owl -o caro-fixed.owl
ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002215 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002215)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002215))]
ERROR Ontology IRIs must be absolute; IRI /imports/pato_import.owl is relative and will be made absolute by prefixing urn:absolute: to it
ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002215 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002215)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002215))]

when pronto is used to import the resulting owl

import pronto
cc = pronto.Ontology("caro-fixed.owl")
/Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: ProntoWarning: XMLSyntaxError occured during import of http://purl.obolibrary.org/obo/caro/imports/ro_import.owl
ProntoWarning)
/Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: ProntoWarning: XMLSyntaxError occured during import of http://purl.obolibrary.org/obo/caro/imports/go_import.owl
ProntoWarning)
/Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: ProntoWarning: XMLSyntaxError occured during import of http://purl.obolibrary.org/obo/caro/imports/pato_import.owl
...

[cmungall]

On 20 Sep 2017, at 3:53, Vince Carey wrote: ERROR Illegal redeclarations of entities: reuse of entity <http://purl.obolibrary.org/obo/RO_0002215> in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002215>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))]

known issue that crops up all the time

ERROR Ontology IRIs must be absolute; IRI /imports/pato_import.owl is relative and will be made absolute by prefixing urn:absolute: to it

this will need fixed

ERROR Illegal redeclarations of entities: reuse of entity <http://purl.obolibrary.org/obo/RO_0002215> in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002215>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))]

ditto to first

when pronto is used to import the resulting owl > > > import pronto > cc = pronto.Ontology("caro-fixed.owl") > /Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: > ProntoWarning: XMLSyntaxError occured during import > of <http://purl.obolibrary.org/obo/caro/imports/ro_import.owl> > ProntoWarning) > /Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: > ProntoWarning: XMLSyntaxError occured during import > of <http://purl.obolibrary.org/obo/caro/imports/go_import.owl> > ProntoWarning) > /Users/stvjc/anaconda2/lib/python2.7/site-packages/pronto/ontology.py:319: > ProntoWarning: XMLSyntaxError occured during import > of <http://purl.obolibrary.org/obo/caro/imports/pato_import.owl> > ...

Ah, the import modules are also functional syntax. OK, next step is to try robot convert -i caro.owl merge -o caro-fixed.owl