Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Failed to parse PSI-MS CV in BioPortal VA

vincentguo gjw_0418 at sina.com
Mon May 16 23:57:10 PDT 2016


Dear BioPortal experts,

    I submitted PSI-MS Controlled Vocabulary (version: 3.86.2, downloaded
from HUPO official website:
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo) into
our BioPortal VA (version2.4) and got an import error.

    Then I replaced the imports with:
import: http://purl.obolibrary.org/obo/pato.obo
import: http://purl.obolibrary.org/obo/uo.obo

    I still got an import error as follows:
Error: UNKNOWN
Message: Error Could not load imported ontology:
<http://purl.obolibrary.org/obo/pato.obo> Cause: Problem parsing
http://purl.obolibrary.org/obo/pato.obo
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) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser at 28ad1e1b
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser at 3ad41caa
3)
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser at 4b08044b
4) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory at 95fd655c
5)
org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser at 58f4fab7
6) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory at 6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.TrigDocumentFormatFactory at 27e81c
8) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory at 937ecd36
9) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory at cd748dc3
10) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory at 3bf24493
11) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory at dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.N3DocumentFormatFactory at 9a5
13) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory at 69b9a3bc
14) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser at 32513f84
15) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.TrixDocumentFormatFactory at 27e82d
16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser at 77b6981b
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser at 6b208eb7
18) org.semanticweb.owlapi.rio.RioParserImpl :
org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory at 264e8d

    Could you please give me some advice on how to solve this problem?

/With best regards,/
/Vincent/



--
View this message in context: http://ncbo-support.2288202.n4.nabble.com/Failed-to-parse-PSI-MS-CV-in-BioPortal-VA-tp4654772.html
Sent from the NCBO Support mailing list archive at Nabble.com.


More information about the bioontology-support mailing list