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[bioontology-support] [bioportal-announce] BioPortal 2.5 Released

Alejandra Gonzalez Beltran a.gonzalezbeltran at cs.ucl.ac.uk
Sun Aug 8 06:42:38 PDT 2010


Dear All,

I forgot to mention that I downloaded BioPortalMetadataKnowledgeBase.owl and
when tried to open it, got the exception below. However, I can access that
URL from a browser and I am also able to load ontologies that are available
online.

I would be grateful if you could help me solving this issue.

Best regards,

Alejandra


Server returned HTTP response code: 503 for URL:
http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd


Full Stack Trace
-----------------------------------------------------------------------------------------

org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server returned
HTTP response code: 503 for URL:
http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
    at
uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:173)
    at
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
    at
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
    at
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:306)
    at
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:180)
    at
org.protege.editor.core.ProtegeManager.loadAndSetupEditorKitFromURI(ProtegeManager.java:179)
    at
org.protege.editor.core.ProtegeApplication.editURI(ProtegeApplication.java:438)
    at
org.protege.editor.core.platform.apple.ProtegeAppleApplication.editFile(ProtegeAppleApplication.java:67)
    at
org.protege.editor.core.platform.apple.AbstractAppleApplicationWrapper$1.invoke(AbstractAppleApplicationWrapper.java:141)
    at $Proxy0.handleOpenFile(Unknown Source)
    at com.apple.eawt.Application$PrivateImpl$4.run(Application.java:502)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)
    at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for
URL: http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
    at
sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1313)
    at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:677)
    at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1315)
    at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1282)
    at
com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:283)
    at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1194)
    at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1090)
    at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:1003)
    at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
    at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:140)
    at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
    at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
    at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
    at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
    at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
    at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
    at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
    at org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:139)
    at
org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:88)
    at
uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
    ... 18 more



On 8 August 2010 11:05, Alejandra Gonzalez Beltran <
a.gonzalezbeltran at cs.ucl.ac.uk> wrote:

> Dear Trish and/or BioPortal support,
>
> I am writing to you with respect to BioPortal and in particular, the
> BioPortal metadata.
>
> I have been read your paper [1] and the information I found online on the
> BioPortal website and the NCBO wiki, about the different functionalities on
> the website and REST services.
>
> In particular, I am interested in the metadata maintained for each of the
> ontologies and read the information at
> http://www.bioontology.org/wiki/index.php/BioPortal_Metadata and I am
> investigating the BioPortalMetadata.owl.
>
> I have not found how I could retrieve the metadata for a particular
> ontology. Could you please point me to documentation about that? I would
> like to be able to retrieve the individuals for the BioPortalMetadata
> ontology for each ontology available in BioPortal.
>
> Also, I would like to understand better how you deal with the mappings
> between ontologies. I have been looking at mappings.rdfs, the mappings
> through the web interface and the REST service retrieving the mappings. For
> example, I would like to have more information on the relationship types. Is
> there any documentation describing mappings.rdfs?
>
> Best regards,
>
> Alejandra
>
> [1] Nucleic Acids Research, 2009, Vol. 37. Web Server Issue.
>
>  --
> Alejandra González-Beltrán, PhD
> Wolfson Institute of Biomedical Research & Department of Computer Science
> University College London
> London WC1E 6BT
> United Kingdom
>
> E-mail: A.GonzalezBeltran at cs.ucl.ac.uk
> Tel: +44 (0)20 7679 0975 (Direct Dial)
> Internal:  40975
> Fax:  +44 (0)20 7209 0470
> Web: http://www.cs.ucl.ac.uk/staff/A.GonzalezBeltran/
> Project Web: http://www.ucl.ac.uk/csm/
>
>
> On 9 June 2010 20:30, Trish Whetzel <whetzel at stanford.edu> wrote:
>
>> The National Center for Biomedical Ontology is pleased to announce the
>> release of *BioPortal 2.5*, a Web-based platform for browsing,
>> visualizing, mapping, and commenting on biomedical ontologies and
>> terminologies.  Our new release of BioPortal includes many new features, Web
>> services, and bug fixes.  BioPortal (http://bioportal.bioontology.org) is
>> a comprehensive repository of biomedical ontologies that enables users to
>> access and share ontologies that are actively used in biomedical
>> communities. Users can publish their ontologies in BioPortal, link
>> ontologies to each other, review ontologies and comment on specific terms,
>> list projects that use ontologies, annotate textual metadata with
>> ontologies, and use Web services to incorporate ontologies or their
>> components into their software applications.
>>
>> Major new features in this release include the following:
>>
>> -       Support for *structured notes and term requests*: Users can now
>> use BioPortal to request that content developers add new terms.  BioPortal
>> provides a structured template for making such requests, allowing users to
>> suggest preferred names, synonyms, and definitions for the requested terms.
>> BioPortal stores the requests as structured notes that are attached to the
>> ontology and that other ontology tools, such as Protégé, will be able to
>> use.
>>
>> -       Support for *email notifications* to interested parties whenever
>> a BioPortal user creates new notes for an ontology of interest. (If you
>> would like to subscribe to notifications about a particular ontology, please
>> send email to support at bioontology.org.  We will have an interactive form
>> to sign-up for notifications shortly.)
>>
>> -       A set of prototype Web services to generate *RDF representation
>> for terms* in ontologies in BioPortal (see documentation [1] for
>> details).
>>
>> -       A prototype end-point for SPARQL access to all ontologies in
>> BioPortal: http://sparql.bioontology.org
>>
>> -       A set of Web services for retrieving instance information for OWL
>> ontologies [1]. We are planning to release a user interface for viewing
>> instances shortly.
>>
>> -       New ontology widgets that developers can embed on their Web sites,
>> including an *ontology tree widget* that allows Web-site authors to
>> present a display of an ontology or an ontology subtree for any BioPortal
>> ontology in any Web page.
>>
>> -       A preview release of *Bio-Mixer*, a mashup tool that provides
>> extremely flexible browsing and exploration of ontologies and their mappings
>>
>>  [1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services
>>
>>
>>  Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> whetzel at stanford.edu
>> http://www.bioontology.org
>>
>>
>>
>>
>> _______________________________________________
>> bioportal-announce mailing list
>> bioportal-announce at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
>>
>> --
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>>
>>
>>
>
>
>
>
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