Errors in BioPortal

[tillmo]

This is a meta ticket for all ontology processing errors ocurring in BioPortal, compiled by Mihai Codescu.

Error 1: "processing"
processing:

• csso
• pdo
• glyco
• imgt-ontology
• nemo
• pma
• bao-gpcr

see #340

update: nemo is now pending.

Error 2: "stack"

Hets exited with status 2:

Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/7dcfcb86021c36e602061e6357d78d08476992f5/raw/BDO.owl Analyzing library BDO logic OWL Analyzing spec BDO#httppurlorgoboowlhumanphenotype Stack space overflow: current size 8388608 bytes. Use `+RTS -Ksize -RTS' to increase it.

• bdo

Update: Bdo is now left pending. Could it be that the flag option was not set when analyzing the ontology? In any case, Ontohub should not keep the ontology pending.

see #411

Error 3: "Could not load imported ontology"

Hets exited with status 1: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/f61494491e1430c099f3ff0a4f71622356d1a433/raw/OAE.owl hets: process stop! ExitSuccess OWL parse error: Could not load imported ontology: http://purl.obolibrary.org/obo/oae/RO_dev_import Cause: http://svn.code.sf.net/p/oae/code/trunk/src/ontology/RO_dev_import org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: http://purl.obolibrary.org/obo/oae/RO_dev_import Cause: http://svn.code.sf.net/p/oae/code/trunk/src/ontology/RO_dev_import at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoad

• oae
• Breast Cancer Grading Ontology
• ovae
• vo
• snp
• Santa Barbara Coastal Observation Ontology
• SO-Pharm
• time event ontology
• cell culture ontology
• epoch
• cognitive paradigm
• dispedia core
• geospecies
• neural motor recovery
• nif
• ontology of physical exercises
• parasite experiment ontology
• pharmacovigilance
• Randomized Controlled Trials
• role ontology

This seems to be a problem with the ontologies themselves. At least for OAE, Protégé says:
File not found: http://svn.code.sf.net/p/oae/code/trunk/src/ontology/RO_dev_import
However, Protégé resumes after displaying this error, and displays the ontology without the imported file. Should Hets do the same?

Yes, see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1213 and #434.

Hets ticket has been solved, now depending on #401.

Error 4: "structured specification not found"

Error: structured specification 'NIFCELL#httpontologyneuinfoorgNIFBackendrobfo11bridgeowl' or 'httpontologyneuinfoorgNIFBackendrobfo11bridgeowl' not found hets: user error (Stopped due to errors)

• nifcell
• mhc
• bioassay
• interaction network ontology
• ogdi
• sweet
• ido
• nif
• pco
• vivo
• aero
• cno
• computer-based patient record ontology
• ddi
• family health history ontology
• nif subcellular

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1211

Update: the HETS ticket has been solved.

Error 5: "unknown AnnotationProperty"

Hets exited with status 1: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/caa81fe6478b80fdecad3fc52d56457c161b274c/raw/ONSTR.owl Analyzing library ONSTR logic OWL Analyzing spec ONSTR#httppurlobolibraryorgobobfoowl *** Error: unknown AnnotationProperty: 'obo:IAO_0010000' hets: user error (Stopped due to errors)

• onstr
• ogi
• mental functioning ontology
• vital sign ontology
• brucellosis
• emotion
• genetic susceptibility factor

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1212

Update: the HETS ticket has been solved.

Error 6: "unknown Datatype"

Hets exited with status 1: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/ff408ee43eba5bb5529fbc1ce2ef83f4a1dcf7d9/raw/LDA.owl Analyzing library LDA logic OWL Analyzing spec LDA#httpwwwsemanticweborgontologies200810languagedisorderautismowl *** Error: unknown Datatype: 'http://www.w3.org/2001/XMLSchema#date' hets: user error (Stopped due to errors)

• language disorder in autism
• medical image simulation
• skin physiology ontology
• nmr
• subcellular anatomy ontology

UPDATE: currently just ontovip, added as a comment to the same ticket below

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1214

The HETS ticket has been solved.

Error 7: "Illegal character in path"

Hets exited with status 1: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/0af0887cb7ad85608dcf09fe6d96f24042103b54/raw/ONTODM-CORE.owl hets: process stop! ExitSuccess OWL parse error: Illegal character in path at index 43: http://kt.ijs.si/panovp/OntoDM.owlOntology(<panovpOntoDMUseCase1.owlOntoDTOntology(<panovpexternal.owlOntology(<panovpexternal_OBI.owlOntology(<obopurl.obolibrary.orgiaoiao.owlexternalDerived.owlprotege-dc.owliao-main.owlexternalByHand.owlontology-metadata.owlobsolete.owlOntology(<oboro1.1external.owl java.lang.IllegalArgumentException: Illegal character in path at index 43: http://kt.ijs.si/panovp/OntoDM.owlOntology(<panovpOntoDMUseCase1.owlOntoDTOntology(<panovpexternal.owlOntology(<panovpexternal_OBI.owlOntology(<obopurl.obolibrary.orgiaoiao.owlexternalDerived.owlprotege-dc.owliao-main.owlexternalByHand.owlontology-metadata.owlobsolete.owlOntology(<oboro1.1external.owl at java.net.URI.create(URI.java:859) at org.coode.xml.XMLWriterImpl.(XMLWriterImpl.java:99) at org.coode.xml.XMLWriterFactory.createXMLWriter(XMLWriterFactory.java:84) at org.coode.owlapi.owlxml.renderer.OWLXMLWriter.(OWLXMLWriter.java:109) at org.coode.owlapi.owlxml.renderer.OWLXMLRenderer.render(OWLXMLRenderer.java:71) at org.coode.owlapi.owlxml.renderer.OWLXMLRenderer.render(OWLXMLRenderer.java:118) at OWL2Parser.parse2xml(OWL2Parser.java:280) at OWL2Parser.parsing_option(OWL2Parser.java:261) at OWL2Parser.main(OWL2Parser.java:124) Caused by: java.net.URISyntaxException: Illegal character in path at index 43: http://kt.ijs.si/panovp/OntoDM.owlOntology(<panovpOntoDMUseCase1.owlOntoDTOntology(<panovpexternal.owlOntology(<panovpexternal_OBI.owlOntology(<obopurl.obolibrary.orgiaoiao.owlexternalDerived.owlprotege-dc.owliao-main.owlexternalByHand.owlontology-metadata.owlobsolete.owlOntology(<oboro1.1external.owl at java.net.URI$Parser.fail(URI.java:2829) at java.net.URI$Parser.checkChars(URI.java:3002) at java.net.URI$Parser.parseHierarchical(URI.java:3086) at java.net.URI$Parser.parse(URI.java:3034) at java.net.URI.(URI.java:595) at java.net.URI.create(URI.java:857) ... 8 more

• Ontology of Core Data Mining Entities
• chemical information ontology

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1215

The Hets ticket has been solved and the ontologies are now properly analyzed on Ontohub.

Error 8: "XML parser: bad frame "

Hets exited with status 1: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/d42af37031e32643a26dcfaa87d653a6837287fd/raw/BOF.owl Analyzing library BOF logic OWL Analyzing spec BOF#httpsqwrlstanfordeduontologiesbuiltins34sqwrlowl Analyzing spec BOF#httpswrlstanfordeduontologies33swrlaowl Analyzing spec BOF#httpwwwowlontologiescomBiodiversityOntologyFullowl hets: XML parser: bad frame

• biodiversity ontology
• sitbac

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1216

Update: the HETS ticket has been solved, sitbac is correctly analyzed, biodiversity ontology seems not to be in Bioportal anymore!

Error 9: "Object not found - failed to find pack entry "

Object not found - failed to find pack entry

• bioportal metadata ontology
• canco
• ecg
• gfo for biology
• onto of medically related social entities
• proteomics data and process provenance
• animal Natural History and Life History Ontology
• ogms
• cdao
• Ontology of Experimental Variables and Values
• suicideonto
• surgical secondary events
• suicideo
• translational medicine ontology
• acgt
• biomedical resource ontology
• drug interaction ontology
• host pathogen interactions ontology
• microarray and gene
• neglected tropical disease
• dataset processing
• mr dataset acquisition
• mental state assessment
• ontology for parasite lifecycle
• rna

Update: the error no longer occurs in Ontohub

Error 10: "no exit status"

Hets exited with status :

• cardiac electrophysiology ontology

Update: this is EP, see below.

Error 11:

Unexpected output: Reading /srv/http/ontohub/releases/20131027194555/tmp/commits/95631115d7be207206a264fc06c5538989c94051/raw/NONRCTO.xml *** Error: missing libname attribute: rdf:RDF

• Non-Randomized Controlled Trials Ontology

http://trac.informatik.uni-bremen.de:8080/hets/ticket/1217

Update: HETS now returns no file for library found, see below. However, Ontohub still gives the same error as above.

Error 12: memory error in HETS

• EP
• nifstd
• sopharm

see HETS ticket #1222

Error 13: no file for library found

• nonrcto
• oae
• dco

see http://trac.informatik.uni-bremen.de:8080/hets/ticket/1224

Update: The ticket has been solved in HETS

Error 14: non-unique name within imported library

• medical image simulation

see trac.informatik.uni-bremen.de:8080/hets/ticket/1230

Update: The ticket has been solved in HETS.

Most of the ontologies now give:
"more than one ontology found"
#401

Validation failed, IRI already taken:

• Interaction Network Ontology
  validation failed error in bioportal #517

Update Feb 7 2014:

• PG::CheckViolation: ERROR: new row for relation "ontologies" violates check constraint "logic_id_check"
  constraint violation in bioportal #576
• Unexpected output: Reading /srv/http/ontohub/releases/20140128004451/tmp/commits/fcf01a6de86d0d7213b03e8e491e25e9faed532f/raw/NONRCTO.xml *** Error: missing libname attribute: rdf:RDF

Bioportal contains a .owl.xml file which is renamed to .xml in Ontohub, and this causes Hets to fail. Calling Hets on the .owl.xml file is successful.

• value too long for type character varying(255)
  http://ontohub.org/repositories/bioportal/ontologies/401
  PG error for ontologies in bioportal: value too long for type character varying(255) #534
• Subprocess ["nice", "/usr/bin/hets", "-o", "pp.xml ... exited with status 137:
  • EP
  • Sopharm
  • nifstd
    http://trac.informatik.uni-bremen.de:8080/hets/ticket/1222
• not a valid OBO Id:

http://ontohub.org/repositories/bioportal/ontologies/2136

http://trac.informatik.uni-bremen.de:8080/hets/ticket/1245

[tillmo]

Christian has closed a number of hets issues. Therefore, I have just updated hets on the server and retried the 84 failed BioPortal ontologies. But now, all of them fail with "no implicit conversion of nil into String", see #433.

[nning]

Did you replace /usr/bin/hets? It is no longer a wrapper shellscript but an ELF binary linked to missing shared libraries. I will repair this and update hets, if necessary.

[tillmo]

Yes, I did (but it already was no script before). Do you think that #433 is caused by the missing shared library?

[tillmo]

aha, #433 has been fixed now...

[mcodescu]

Now Bioportal gives a new type of error:

Unexpected output: Reading file /srv/http/ontohub/releases/20131027194555/tmp/commits/b0eea2c5d5d34eb9f1ddd496b3ec14bf721bb121/raw/OOEVV.owl *** Error: empty input file: /srv/http/ontohub/releases/20131027194555/tmp/commits/b0eea2c5d5d34eb9f1ddd496b3ec14bf721bb121/raw/OOEVV.owl

for a number of ontologies, among them:
http://develop.ontohub.org/repositories/bioportal/ontologies/8804/versions
http://develop.ontohub.org/repositories/bioportal/ontologies/8873/versions
http://develop.ontohub.org/repositories/bioportal/ontologies/8817/versions
http://develop.ontohub.org/repositories/bioportal/ontologies/8876/versions

[corny]

Meanwhile the given ontology ids do not exist any more.

[tillmo]

at http://develop.ontohub.org/repositories/bioportal/errors you get a good overview of the errors.

• the main problem is "more than one ontology found". Parsing single ontologies with imports correctly (in OWL, CommonLogic) #401 and Add present flag to Ontology #441 are just being solved
• the second largest problem are the pending ontologies, see Ontology processing indefinitely #340 (currently, there are many of them because @0robustus1 seems to just have restarted processing those for the main problem, so please wait a few hours)
• the rest are minor problems, @mcodescu is taking care

[tillmo]

@mcodescu, what is the current status?

[mcodescu]

Bioportal has the same errors as in Feb 7th, I retried some ontologies and I get the same errors. #576 needs to be solved and we have to wait for Christian experiments for speeding up parsing of XML files in Hets.

[mcodescu]

Update March 18th:

• 46 ontologies with logic_id_check error, issue constraint violation in bioportal #576
• 2 ontologies that take too long on HETS (I didn't retry EP), HETS trac issue 1248
• 1 ontology with too long strings, issue PG error for ontologies in bioportal: value too long for type character varying(255) #534

[tillmo]

3 errors remaining, but there are other tickets for these