obo-behavior / behavior-ontology Goto Github PK

Importing the whole of ChEBI is not useful.

<owl:Ontology rdf:about="&obo;behavior.owl">
    <oboInOwl:remark rdf:datatype="&xsd;string">2012-07-09</oboInOwl:remark>
    <owl:imports rdf:resource="&obo;chebi.owl"/>

...

Conciousness: ""Behavior related to a variety of aspects of the relationship between the mind and the world with which it interacts." [wikipedia:Consciousness]"
Wakfefulness: ""Behavior related to the state of being conscious and engages in a coherent cognitive and behavior responses to the external world." [NBO:SD, wikipedia:Wakefulness]"

Many animals sleep. For many of those species, most researchers would not be comfortable with use of the term 'mind'. And conciousness obviously has connotations far beyond the state of wakefulness.

• TODO Move out wakefulness from under conciousness

.obo is being built by berkeleybop, remove from repo to avoid confusion.

For new term requests, please provide the following information:

Preferred term label

trapping behavior

Synonyms

Textual definition

a predator behavior involving subduing prey using a structure or modification of the environment created by the predator for that purpose

Suggested parent term

predator behavior http://purl.obolibrary.org/obo/NBO_0000089

Attribution
http://orcid.org/0000-0002-2908-3327

Term is needed for ecocore EcologicalSemantics/ecocore#2

Preferred Name  
behavioral control of defecation

Definitions     
The expulsion of feces from the rectum. [wikipedia:defecation]

ID  
NBO:0000039

Full Id 
http://purl.obolibrary.org/obo/NBO_0000039

Not sure that all animals that defecate have a rectum.

Original issue reported on code.google.com by [email protected] on 24 Feb 2013 at 9:20

Make specific to organisms with nervous systems?

Bjoern: Reactions are in response to external stimulus.  Actions are not.

Need to define internal stimulus.  Does it include neural processes themselves? 
 If so 'stimulus' is so broad as to be almost meaningless.

Original issue reported on code.google.com by [email protected] on 24 Feb 2013 at 8:55

NBO includes:

• NBO terms with xrefs to GO ids
• GO terms used compositionally to define NBO terms via some class restriction (relationship).

These need to be harmonised, or if justified, documented.

http://purl.obolibrary.org/obo/BFO_0000056

I'm trying to do a release for another ontology and ran into this error when doing the make all. Details are below:

owltools http://purl.obolibrary.org/obo/nbo.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o mirror/nbo.owl
[Fatal Error] :1:50: White spaces are required between publicId and systemId.
2018-08-31 17:06:16,745 ERROR (CommandRunner:4646) could not parse:http://purl.obolibrary.org/obo/nbo.owl
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/nbo.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. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@5c18016b
2. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@339bf286
3. org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@33e01298
4. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5. org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1d71006f
6. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
9. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
13. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14. org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15. org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@58783f6c
16. org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@ea27e34
17. org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@3bb9efbc
18. org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
19. org.coode.owlapi.obo12.parser.OWLOBO12Parser@4837595f

Detailed logs:

Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@5c18016b
Stack trace:
org.xml.sax.SAXParseException; systemId: http://purl.obolibrary.org/obo/nbo.owl; lineNumber: 577722; columnNumber: 67; Premature end of file. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Premature end of file. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.endOfFileHook(Unknown Source)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@339bf286
Stack trace:
Attribute not found: IRI (Line 53) org.semanticweb.owlapi.owlxml.parser.OWLElementHandler.ensureAttributeNotNull(PARSER_OWLXMLVocabulary.java:381)
org.semanticweb.owlapi.owlxml.parser.OWLElementHandler.getIRIFromAttribute(PARSER_OWLXMLVocabulary.java:214)
org.semanticweb.owlapi.owlxml.parser.OWLAnnotationPropertyElementHandler.attribute(PARSER_OWLXMLVocabulary.java:1193)
org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.startElement(OWLXMLParserHandler.java:482)
org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@33e01298
Stack trace:
Encountered " " "" at line 1, column 1.
Was expecting one of:
"Ontology" ...
"Prefix" ...
(Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:84)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Encountered " " "" at line 1, column 1.
Was expecting one of:
"Ontology" ...
"Prefix" ...
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:3443)
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:3363)
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:192)
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:171)
org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:82)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
IRI included an unencoded space: '32' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)

Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1d71006f
Stack trace:
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:108)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
IRI included an unencoded space: [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
org.openrdf.rio.ntriples.NTriplesParser.reportError(NTriplesParser.java:631)
org.openrdf.rio.ntriples.NTriplesParser.parseUriRef(NTriplesParser.java:423)
org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:336)
org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123)
org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102)
org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:60)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
Stack trace:
org.openrdf.rio.RDFParseException: Found IOException during parsing [line 1, column 2] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Found IOException during parsing [line 1, column 2] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
org.openrdf.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:155)
org.openrdf.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:96)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
IRI included an unencoded space: [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
org.openrdf.rio.ntriples.NTriplesParser.reportError(NTriplesParser.java:631)
org.openrdf.rio.ntriples.NTriplesParser.parseUriRef(NTriplesParser.java:423)
org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:336)
org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280)
org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191)
org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:130)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
IRI included an unencoded space: '32' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
org.openrdf.rio.trig.TriGParser.parseGraph(TriGParser.java:132)
org.openrdf.rio.trig.TriGParser.parseStatement(TriGParser.java:119)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
Stack trace:
org.openrdf.rio.RDFParseException: File does not contain a binary RDF document org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
File does not contain a binary RDF document org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:424)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:693)
org.openrdf.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:87)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
Stack trace:
org.openrdf.rio.RDFParseException: Could not parse JSONLD org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Could not parse JSONLD com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:69)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
Unexpected character ('<' (code 60)): expected a valid value (number, String, array, object, 'true', 'false' or 'null')
at [Source: java.io.BufferedReader@6c44052e; line: 1, column: 2] com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1702)
com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:558)
com.fasterxml.jackson.core.base.ParserMinimalBase._reportUnexpectedChar(ParserMinimalBase.java:456)
com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1906)
com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:749)
com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:107)
com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:88)
com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:68)
com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:65)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
IRI included an unencoded space: '32' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
Stack trace:
org.openrdf.rio.RDFParseException: White spaces are required between publicId and systemId. [line 1, column 50] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
White spaces are required between publicId and systemId. [line 1, column 50] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
org.openrdf.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1286)
org.openrdf.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1443)
org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source)

Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
Stack trace:
org.openrdf.rio.RDFParseException: White spaces are required between publicId and systemId. [line 1, column 50] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
White spaces are required between publicId and systemId. [line 1, column 50] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123)
org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90)
org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
White spaces are required between publicId and systemId. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source)
org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source)
org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)

Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@58783f6c
Stack trace:
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:94)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Encountered "" at line 1, column 1.
Was expecting one of:
org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1548)
org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1430)
org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:153)
org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:87)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)

Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@ea27e34
Stack trace:
LINENO: 1 - Could not find tag separator ':' in line.
LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
LINENO: 1 - Could not find tag separator ':' in line.
LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501)
org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897)
org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528)
org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521)
org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:504)
org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:377)
org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:335)
org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281)
org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76)
org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83)

Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@3bb9efbc
Stack trace:
org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:278)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Encountered " ">" " "" at line 1, column 1.
Was expecting:

org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:3187)
org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:3040)
org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:141)
org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:275)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
Stack trace:
org.openrdf.rio.RDFParseException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:111)
org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. org.semarglproject.rdf.rdfa.RdfaParser.processException(RdfaParser.java:1141)
org.semarglproject.source.XmlSource.process(XmlSource.java:50)
org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
White spaces are required between publicId and systemId. org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
org.semarglproject.source.XmlSource.process(XmlSource.java:48)
org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)

Parser: org.coode.owlapi.obo12.parser.OWLOBO12Parser@4837595f
Stack trace:
org.coode.owlapi.obo12.parser.TokenMgrError: Lexical error at line 1, column 22. Encountered: "\n" (10), after : "" org.coode.owlapi.obo12.parser.OWLOBO12Parser.parse(OWLOBO12Parser.java:123)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
Lexical error at line 1, column 22. Encountered: "\n" (10), after : "" org.coode.owlapi.obo12.parser.OBOParserTokenManager.getNextToken(OBOParserTokenManager.java:973)
org.coode.owlapi.obo12.parser.OBOParser.jj_ntk(OBOParser.java:289)
org.coode.owlapi.obo12.parser.OBOParser.TagValuePair(OBOParser.java:74)
org.coode.owlapi.obo12.parser.OBOParser.Header(OBOParser.java:40)
org.coode.owlapi.obo12.parser.OBOParser.parse(OBOParser.java:14)
org.coode.owlapi.obo12.parser.OWLOBO12Parser.parse(OWLOBO12Parser.java:100)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:217)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)

at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:254)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1250)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1204)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1104)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1060)
at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
at owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4634)
at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)

make: *** [mirror/nbo.owl] Error 1
Annes-MacBook-Pro-2:ontology annethessen$

Dear NBO team,

We've created an ontology for core ecological entities (ECOCORE) over at this repo.

We'll need ethology semantics and will be importing NBO. We'll likely have some requests for NBO - are you able to address these in the near-term? If not, we'll create some classes in ECOCORE and mark them as "to be surrendered to NBO" or similar, in anticipation of new class creation here.

Looking forward to developing!

For new term requests, please provide the following information:

Preferred term label

ambush behavior

Synonyms

Textual definition

a predator behavior involving a surprise attack on unsuspecting prey. The predator remains in one place and waits for prey to come near. The predator conceals itself and then subdues its prey with its own body or body parts.

Suggested parent term

predator behavior http://purl.obolibrary.org/obo/NBO_0000089

Attribution
http://orcid.org/0000-0002-2908-3327

Term is needed for ecocore EcologicalSemantics/ecocore#2

In the file downloaded from http://purl.obolibrary.org/obo/nbo.owl, the ontology IRI is http://purl.obolibrary.org/obo/ (rather than http://purl.obolibrary.org/obo/nbo.owl as expected). This ontology has version IRI http://purl.obolibrary.org/obo/nbo/releases/2018-02-02/nbo.owl.

May be handled currently as feeding behavior but probably belongs elsewhere.

is the intention that these are disjoint?

That might seem a natural interpretation given

 NBO:0000243 ! behavioral phenotype [DEF: ""An observable characteristic of the behavior of an organism." [NBO:RH]"]
 NBO:0000313 ! behavior process [DEF: ""The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO:0007610]"]

and an interpretation of 'characteristic' as being something attribute-like.

It seems the hierarchies are largely disjoint, with the exception of: NBO:0000096 ! agoraphobia behavior

it seems there shoukd either be zero or a lot more crossings

'consciousness' also seems not to really be a behavior. The same goes for most 
of its direct children.  'Asleep' might be an exception, but this actually 
appears elsewhere in the ontology as 'sleeping behavior' which does seem more 
directly to capture the behavior aspect. 

Original issue reported on code.google.com by [email protected] on 1 Jun 2011 at 12:23

--/ NBO:0000000 ! behavior
----is_a NBO:0000243 ! pathological behavior
------is_a NBO:0000256 ! mood disorder
--------is_a NBO:0000258 ! bipolar disorder ***  [DEF: "A mood disorder 
formerly characterised by alternating periods of mania and depression (and in 
some cases rapid cycling, mixed states, and psychotic symptoms)."]

disorders shouldn't be in NBO. Perhaps change these to "disorder-related 
behavior"? Or just obsolete and use another ontology

Original issue reported on code.google.com by [email protected] on 30 May 2011 at 4:19

Many definitions use the phrases: 'related to' and 'associated with'.  These 
are two vague.  All cases should be removed or replaced with something more 
specific.

e.g.-  In this case, related to doesn't seem to add anything.


[Term]
id: NBO:0000078
name: post-mating behavior
is_a: NBO:0000010 ! reproductive behavior
def: "Behavior related to the specific actions or reactions of an organism 
following mating." [GOC:bf]
xref: GO:0045297
>
"The specific actions or reactions of an organism following mating." [GOC:bf]

In other cases it may mean 'results in'

[Term]
id: NBO:0000056
name: walking behavior
is_a: NBO:0000359 ! terrestrial locomotory behavior
def: "Behavior related to surface locomotion." [NBO:GVG]
xref: GO:0007628

A movement behavior that results in surface locomotion?

Original issue reported on code.google.com by [email protected] on 24 Feb 2013 at 9:51

I don't think that "pure" feelings or emotions should be included under 
emotional behavior, since there is usually no characteristic behavior for such 
states.  

Examples are 
'pleasure', 'frustration', 'distress'...

For contrast, good examples of emotional behavior include 
'laughing behavior',
'crying behavior' 

From EMO (the emotion ontology) we can link to the relevant emotional behaviors 
in the behavior ontology

Original issue reported on code.google.com by [email protected] on 1 Jun 2011 at 12:21

http://en.wikipedia.org/wiki/Autotomy

Original issue reported on code.google.com by [email protected] on 23 Apr 2012 at 9:04

The import chain brings in chebi.owl which is excessive

Consider using https://github.com/cmungall/ontology-starter-kit to set up the repo in a more standard format

• Find the Assay Ontology that is in progress
• Ensure that they are well-supported by this ontology

ID: NBO:0000446
Preferred Name : visual pursuit
Definitions: Selectively track a moving object. [NBO:GVG]


1. Definition needs to include mention of vision.  Current term applies to bats 
using echolocation.
2. Needs to be subclass of visual behavior
3. Should not be a subclass of eye movement - as not all animals that can 
visually track can move their eyes.

General question: 
This is under body part movement - should visual pursuit be treated more 
generally, encompassing tracking via whole body movement.

Original issue reported on code.google.com by [email protected] on 24 Feb 2013 at 8:48

This is a list of terms from ABO that we (Anne, Sue, Peter) wish to include in NBO. These
terms are all subsumed by (terminal on the tree relative to) existing NBO terms. There
are a small number of terms that we propose to insert within the NBO hierarchy, but
those will come in a later issue.

Each of these terms has been assigned an identifier from the block of identifiers assigned
to @dosumis during the workshop in DC in October 2015. We have used only 300 of
this range, so there will be plenty for VFB to use in the future. These include approximately
10 terms that were not in the version of ABO that we used for the preliminary merge at that
workshop. I have manually assigned these the next IDs in sequence.

Terms to add

Definitions

Agnostic alarm - Alarm behavior triggered by agonistic actions or postures

Agnostic buffering - Carrying or manipulation of infants or equivalent items to reduce chances of aggression on carrier by other animals

Agnostic chase - Chasing of one animal by another during an agonistic conflict

appeasement - Behaviors that appear to signifiy lack of hostility and to reduce chances of attack

assessment behavior - A behavior on the part of one individual associated with evaluating the fighting ability or correlates of fighting ability of a potential opponent

capturing prey - Behavior that results in ending flight of prey with successful predation

coercion - Forcible alteration of behavior of one animal by another.

contact aggression - Agonistic behavior involving direct physical contact including (but not limited to) biting, kicking, grabbing.

displacement behavior - An acitvity that seems irrelevant to its behavioral context to a human observer and often occurs when its performer is in a conflict situation

escalation - Increasing intensity of directed agonistic behavior.

exclusion - Behavior that serves to exlude an animal from a group

injure (injuring) - Behavior in which one animal causes bodily damage to another.

kill (killing) - Behavior in which one animal causes the death of another.

threat - Behavior that signifies hostility and predicts an increased probability of attack

triumph - Display behavior by the winner of a prior agonistic contest.

Aposematism - Conspicuous postures or signals (often coloration) that potential predators learn to associate with strong defense mechanisms of performer

bluff - Threat that will not be acted upon.

create refuge - Construction of a structure in which builder can benefit from reduced predation risk and/or environmental stress.

misdirect predator - Behaviors directed towards presumed predators to redirect their attention away from a location of importance to the performer

deploy defense - use of behavioral tactics or chemical weapons to deter predation. Example: flashing eye spots (behavioral tactic) or expulsion of noxious liquid (chemical)

(predator) detection notification - Postures or signals that can communicate to predator that it has been detected by performer

display condition (to predator) - Performance of behaviors that demonstrate physical condition of performer to a detected predator

distress signaling - Signals emitted by an animal trapped or captured by a presumed predator

enhance crypsis - Behaviors that reduce detectability of performer against background

feign death - Become immobile and reduce other evidence of living state

flee - Depart [from] current location of predator

inspect predator - Conspicuous orientation towards and/or approach to detected predator

mimicry enhancement - Behaviors, anatomical structures, or signals that imitate aposematic animals, plants, or inanimate objects that are undesirable to predators of performer

jamming - Emission of signals in such a way as to prevent effective use of signals emitted by other parties

occupy refuge - Currently reside in constructed or existing structure that provides reduced predator and/or environmental risk

promote confusion - Erratic movements or similar behaviors that would confuse a predator.

reduce activity - Halting or diminution of activity to minimize detection by predator.

attack predator - Perform physically violent acts on a presumed predator

vigilance - Surveillance for presence or approach of predators

warn other prey - Postures or signals that alert other animals to presence or approach of a predator.

Nutrient acquisition - Behaviors related to acquisition and utilization of external resources.

Nutrient locating - Movement directed to the detection of new resources.

Nutrient preparation - Behavior that precedes and facilitates attaining food

Resource advertisement - Postures or signals performed to other animals to indicate the presence, and in some cases, the location, quantity, and quality, of a resource

Social acquisition of food - Obtaining food that has been procured by other conspecifics or heterospecifics.

capturing (behavior) - Suite of behaviors involved in securing a prey item once it has been located.

chase prey - Active pursuit of fleeing prey.

capturing prey - Behaviors that result in ending flight of prey with successful predation.

construct capturing device - Building of a trap, web, net, or other structure to help ensnare potential food items

flush prey - Behaviors in which predator forces potential prey to emerge from cover.

stalk prey - Approach to prey in manner designed to avoid early detection by prey.

aiding digestion - consumption of specific compounds that facilitate processing of food items

dealing with toxins - The identification, avoidance, or neutralization of toxic substances in food

food storage - Caching or hoarding of food for later use and for protection from competitors, or use of specific substrates for cultivation.

caching behavior - The act of putting a food resource in a location in which it can be stored or protected until a future time

follow trail to resource - Locomotion to a resource guided by visual or olfactory cues created by a prior finder and/or user of that resource.

food exposure - Behaviors that reveal a hidden food resource, such as digging, cracking, or breaking.

recovery from cache - Removal of food resource from previously-stored supply of food.

food extraction - Removal of food items from location by use of appendage or tool.

food processing - Behaviors that prepare food for consumption, such as nut-cracking or peeling

suitability assessment - Sensory assessment of a resource, (usually using olfaction or taste), for suitability of subsequent usage

beg food - Perform behaviors that may induce one or more other animals to share food with the performer

scrounge - Uninvited taking of food from another animal

scavenge - Behavior associated with locating and acquiring food that has been killed or procured by another animal.

share food - Behaviors in which animals solicit or allow other animals to utilize a resource they currently control

cooling behavior - Behaviors that serve to reduce body temperature as by moving to shade or panting

mate finding behavior - Active search for possible mates

sexual interference - Usually interference by members of one sex in the completion of courtship or mating activities by one or more members of the same sex

mate rejection - Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor.

sexual harassment - Any of several behaviors directed towards one animal unwilling to mate by another eager to do so

hunt for mate - active searching of potential mate

reproductive status assessment - Assessment of cues and signals from encountered individual to determine reproductive condition

mate sampling - General category of behaviors including sampling of medium to detect presence of possible mates, and sampling of encountered individuals to determine mate suitability

insert genital plug - Behavior associated with deposition of material by male following ejaculation to block access to female's reproductive tract during her future matings.

sperm scraping - use of specialized male organs to remove sperm already deposited in female's reproductive tract.

breeding site selection - Actions resulting in establishment or use of one locale for reproductive activity

courtship begging - Behavior by one animals soliciting food provision by a potential mate

courtship feeding - provision of food to a potential mate

mating appeasement - Behavior that serves to demonstrate non-aggressive intent by one member of a courting or potentially mating pair to the other.

sexual cannibalism - Consumption of one member of a mating pair, usually the male, usually after the mating

mating solicitation - Performance of a behavior that indicates the performer's willingness to mate or bond

broadcast advertisement - Signal or behavior that reveals presence of the signaller directed to multiple receivers and not limited to particular receivers

build display structure - Creation of or modification of a structure or area that is used in attraction of mates

mate guarding - One member of a recently mating pair prevents the other from subsequent matings with other individuals

pair affirmation - displays or other behaviors performed by pairs in longer term pair bonds to advertise relationship to each other and to other animals nearby

mouth brooding - Process of retaining developing eggs in the mouth cavity

gamete release function - Facilitating release or transfer of gametes

facilitating oviposition - Deposition of eggs either into the medium, or onto a substrate

insemination - Insertion of sperm not in a spermatophore into female body

mating amplexus - Spawning in which male and female are clasped or attached to ensure close proximity of released gametes

spawning - Release of gametes one or both sexes into the ambient medium

spermatophore deposition - Deposition of spermatophore either on substrate or in body of female

agnostic alarm - Alarm behavior triggered by agonistic actions or postures

Mentioning @swmargulis here so she sees this issue.

For new term requests, please provide the following information:

Preferred term label

hunting behavior

Synonyms

Textual definition

a predator behavior involving actively stalking prey over a distance

Suggested parent term

predator behavior http://purl.obolibrary.org/obo/NBO_0000089

Attribution
http://orcid.org/0000-0002-2908-3327

Term is needed for ecocore EcologicalSemantics/ecocore#2

Liquid aversion is, in my opinion, falsely asserted to be a subclass of alcohol aversion. (Liquid preference and regulation of alcohol preference are correctly classified). It should be the other way around.

I would also like to point out the slightly idiosyncratic definitions of these two classes: Why does the definition of liquid aversion (and preference!) contain a restriction on the decreased rate quality (towards some liquid consumption), while the respective definitions involving alcohol do not? Lastly, and least important, the human-readable definition of "regulation of alcohol preference behavior" contains a typo (alchohol instead of alcohol).

GO:0060082 ! eye blink reflex

or demote:

synonym: "blink reflex" EXACT []

Original issue reported on code.google.com by [email protected] on 14 Dec 2011 at 8:35

"ID: NBO:0000040
Preferred Name: behavioral control of urination

Synonyms : micturition EXACT []

Definitions     
The regulation of body fluids process by which parasympathetic nerves stimulate 
the bladder wall muscle to contract and expel urine from the body. 
[wikipedia:urination]:

Reference to 'parasympathetic nerves' and 'bladder wall' probably makes this 
too species specific.

Original issue reported on code.google.com by [email protected] on 24 Feb 2013 at 9:17

  is_a NBO:0000266 ! cognitive behavior phenotype
   is_a NBO:0000655 ! sensation behavior phenotype
    is_a NBO:0000656 ! somatic sensation related behavior phenotype
     is_a NBO:0000229 ! vestibular behavior phenotype
      is_a NBO:0000591 ! motor coordination phenotype
       is_a NBO:0000590 ! ataxia *** 

@memartone does not believe ataxia to be cognitive

What steps will reproduce the problem?
1. browse to 'visual behavior phenotype' (NBO_0000659)
2. observe parentage (subsuming terms)
3.

What is the expected output? What do you see instead?
'sensation behavior phenotype' seems reasonable, second subsuming term 
'reproductive behavior phenotype' seems to subsume some but not all of this 
class (not requesting that we reify the intersection at this time)

What version of the product are you using? On what operating system?
2012-07-09; viewed using Protege 4.3

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 1 Aug 2014 at 9:57

This is a list of NBO terms for which @aclark-binghamton-edu and @swmargulis have identified synonyms in ABO, however the synonyms are likely either broader or narrower than the NBO terms. These ABO terms might simply added as synonyms with the appropriate scope or possibly as new terms inserted into the NBO hierarchy.

I am posting this list as a request for comment on what to do with these specific ABO terms.

There are other ABO terms that we do want to add to NBO as new terms. I will assemble a list of those terms in separate issues (one for leaf terms and one for terms to be inserted) and then generate pull requests for these changes.

What steps will reproduce the problem?
1. browse to this term (behavior process -> kinesthetic behavior ->voluntary 
movement behavior -> head movement

What is the expected output? What do you see instead?
multidirectional head movement
mutlidirectional head movement

What version of the product are you using? On what operating system?


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 31 Jul 2014 at 7:09

A list of propose NBO-ABO merges.

• For each case,
  • NBO parentage should be considered, NBO flattened where needed
  • ABO subClasses should have names changed to be less ambigous when considered in isolation
  • Old names need to be retained as synonyms with some dedicated type
  • All ABO terms moved across for merge must have NBO IDs in a dedicated ID range

flee SubClassOf anti-predation

flee > flee predator

• Terms to merge

• Antipredation -> NBO_0000087 ; antipredation behavior

• Terms from ABO to use directly

• maintenance ( -> maintenance behavior).

• NBO Terms to move under ABO terms

• nest building under refuge creation and maintenance

  see https://docs.google.com/spreadsheets/d/1GO1ZoZ0MWDPj4mKnwUdIAflmNxZywidjLp-r3KImWrI/edit#gid=2017721846
  ...

ABO contains terms that are not behaviors. Many of these are equivalent to terms in GO. For all of these, terms should be obsoleted and GO terms used in their place. This should be documented in recommendations for curation.

Life history transitions are the obvious case.

• metamorphosis is in GO (there are also developmental stage ontologies that should be checked.)
  • Need to:
    • distinguish behaviors associated with life-history transition
  • Neural regulation of life-history

Other examples:

• body colour change: Should be in GO. But body color change behavior (see cephalopods and chameleons) belongs in NBO/ABO. (Question: What about revealing a color that is already on the body but not visible)?

The definition of social learning seems to limit it to humans.  However, there 
is a long history of study of social learning in animals (e.g., Zental and 
Galef 1988).  The definition should be updated to reflect this.

Original issue reported on code.google.com by [email protected] on 10 Jun 2011 at 3:22

NBO pulls in a lot of old versions of ontologies that are causing trouble for importing ontologies. Along with many other OBO ontologies, we are adding base products of ontologies everywhere that contain only the axioms that are owned by the ontology, and omitting any imports of axioms that are owned by another ontology (such as axioms from GO or UBERON). I could do this, perhaps even move NBO to the new ODK release pipeline, I just need write access to NBO. @cmungall @dosumis

The recently added nbo.obo file is empty. Attempts to convert current nbo.owl into nbo.obo yielded similar kinds of masking errors as was before.

Could you make the latest nbo ontology also available in obo format? I am unable to convert nbo.owl to nbo.obo by either robot or Protege. Thanks!

For new term requests, please provide the following information:

Preferred term label

predator avoidance behavior

Synonyms

Textual definition

an avoidance behavior engaged in by prey that reduces the success of a predator without the prey actually attacking the predator

Suggested parent term

avoidance behavior http://purl.obolibrary.org/obo/NBO_0000635

Attribution

http://orcid.org/0000-0002-2908-3327

Term is needed for ecocore EcologicalSemantics/ecocore#2

To one of the terms below:

.....is_a NBO:0000013 ! locomotory behavior
......is_a NBO:0000368 ! climbing behavior ***
.......is_a NBO:0000364 ! arboreal locomotion behavior ***
........is_a NBO:0000365 ! brachiation
.......is_a NBO:0000513 ! climbing stairs

also the def of NBO:0000368
"Behavior related to the ascending a steep object"

is brachiation really ascending a steep object?

And isn't gliding through trees an arboreal locomotion behavior? But this isn't 
climbing. Seems to be combining two axes?

 * The environment of the locomotion (use ENVO here for logical defs)
 * The actual mechanics

Original issue reported on code.google.com by [email protected] on 11 Feb 2013 at 8:47

NBO is broken in its division into involuntary vs voluntary movements

Most (all?) behaviors under 'reflexive behavior' are 'body part movements'. But 'body part movement' is classified under 'voluntary movement behavior'.

Solution: Move 'body part movement' under 'kinesthetic behavior'. If we need voluntary version of all the behaviors under this, these should become new NBO terms. Where reflexes involve some specific body part movement, that should be second parent class to the reflex term. (A compositional approach would help here).

Migration in found in many groups of animals, such as birds, fish, or insects, 
but there is no term for behavior associated with migration in NBO.  I would 
recommend adding this a migratory behavior, rather than migration, which is a 
population level phenomenon that belongs in PCO.

Original issue reported on code.google.com by [email protected] on 4 Mar 2013 at 7:40

You have:

xref: GO:0001967 "suckling behavior"

This is incorrect syntax. You should have

xref: GO:0001967 ! suckling behavior

(you can have whatever you like after the "!", but of course it should be the 
GO label, there are tools that will do this automatically).

You should also have a header:

treat-xrefs-as-equivalent: GO

Then, according to the OBO specification, the GO xrefs are treated as 
equivalence axioms. Tools such as Oort will generate the correct OWL

Original issue reported on code.google.com by [email protected] on 14 Dec 2011 at 8:34

Upon reviewing the NBO, this term seems unnecessary, as there are hardly any 
behaviors that wouldn't stem from insight.

Consider obsoleting?

Original issue reported on code.google.com by [email protected] on 10 Feb 2015 at 1:57

posture seems more of a state/quality than a behavior

   is_a MBO:0000317 ! vestibular behaviour [DEF: "Behaviour related to the awareness of body balance and movement."]
      is_a MBO:0000355 ! posture ***  [DEF: "Intentionally or habitually assumed arrangement of the body and its limbs."]
       is_a MBO:0000356 ! body posture ***  [DEF: "Intentionally or habitually assumed arrangement of the body."]
       is_a MBO:0000357 ! limb posture ***  [DEF: "Intentionally or habitually assumed arrangement of the limbs."]
       is_a MBO:0000358 ! resting posture ***  [DEF: "Intentionally or habitually assumed arrangement of the body and its limbs in inactivity."]


"posturing behavior" is not really right...

maintenance of posture?

Original issue reported on code.google.com by [email protected] on 22 Apr 2011 at 5:24

Can you add class such as 'supination'. See:

http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion

From there I can request specific terms such as "forearm supination", "jaw 
adduction" etc

Original issue reported on code.google.com by [email protected] on 14 Aug 2012 at 11:56

I wouldn't say that 'intelligence' and its children are types of behavior.  

Not only doesn't it seem to me
to be a kind of behavior, but also not a kind of cognition (its
immediate is-a parent).  Don't we remain intelligent even if we are
not thinking about anything?  

It seems rather a capability (disposition) than a behavior (process).

Original issue reported on code.google.com by [email protected] on 31 May 2011 at 2:27

Greetings NBO!

At ENVO, @TaskeHAMANO and I are working on adding some classes such as pasturable land that would benefit from the addition of "grazing behaviour".

I would imagine this is useful for ontologies like ECOCORE too.

Suggested definition:
"A feeding behavior during which an animal ingests biomass produced by a plant or other primary producer"
dbxref: https://en.wikipedia.org/wiki/Grazing

We can define "primary producer" in ECOCORE

This will crosslink with AgrO's treatment of the agricultural practices associated with this behaviour: AgriculturalSemantics/agro#32

Thoughts?

• A pattern combining a behavioral act and its function, e.g. locomotion for anti-predation