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obophenotype / caro

Working repository for v2 of CARO
Creative Commons Attribution 4.0 International
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caro.owl is not xml/rdf #14

Open vjcitn opened 7 years ago

vjcitn commented 7 years ago

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

cmungall commented 7 years ago

See also: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/360

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

vjcitn commented 7 years ago

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 commented 7 years ago

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