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#367 Serving ontologies from github
I would like to serve ontologies from github
For example, this cephalopod ontology:
However, I don't want to hardcode this URL or to have it be the Ontology IRI.
I set up a PURL that redirects to the above URL
This is fairly standard practice with google code etc.
When I wget the above (with --no-check-certificate) it gets an OWL RDF/XML file which is parsed without difficulty by the OWLAPI
However, when I try and use the URL directly (or in an import) I get:
2013-05-03 17:39:50,868 INFO owltools.io.ParserWrapper$1.startedLoadingOntology(ParserWrapper.java:70) - Start loading ontology: http://purl.obolibrary.org/obo/uberon/experimental/ceph.owl from: http://purl.obolibrary.org/obo/uberon/experimental/ceph.owl
2013-05-03 17:39:52,012 INFO owltools.io.ParserWrapper$1.finishedLoadingOntology(ParserWrapper.java:77) - Finished loading ontology: null from: http://purl.obolibrary.org/obo/uberon/experimental/ceph.owl
could not parse:http://purl.obolibrary.org/obo/uberon/experimental/ceph.owl Exception:org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/uberon/experimental/ceph.owl
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:
1) RDFXMLParser
2) OWLXMLParser
3) OWLFunctionalSyntaxOWLParser
4) TurtleOntologyParser
5) OWLOBOParser
6) KRSS2OWLParser
7) ManchesterOWLSyntaxOntologyParser
Detailed logs:
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Parser: RDFXMLParser
org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
--------------------------------------------------------------------------------
Parser: OWLXMLParser
org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
--------------------------------------------------------------------------------
Parser: OWLFunctionalSyntaxOWLParser
Encountered " <ERROR> "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)
--------------------------------------------------------------------------------
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
--------------------------------------------------------------------------------
Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""
--------------------------------------------------------------------------------
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\"> "" at line 1, column 1.
Was expecting:
<EOF>
--------------------------------------------------------------------------------
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)
Thanks for the report, this is easier to replicate than 319.