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From: Gerhard M. <may...@ru...> - 2012-08-30 10:46:20
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Hallo Mr. Gkoutos, I'm maintaining the psi-ms.ontology (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). Since the last release (29:08:2012) of the unit.obo file I get the following errors when I try to load my ontology by OBO-Edit 2.2: Load Error, line 547 48 unrecognized parent terms: line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) I saw that in former versions of the unit ontology there was the import statement import: http://purl.obolibrary.org/obo/pato.obo which is now missing resp. replaced by ontology: uo ontology: pato I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) ontology: xyz was introduced as a new docuemnt header tag. But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. In addition you specified the old 1.2 format in your unit.obo file: format-version: 1.2 which should be changed to format-version: 1.4 in case you want to use the new format. Best Regards, Gerhard -- ------------ Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Kairos GmbH Universitätsstraße 136 44799 Bochum Email: ger...@ka... |
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From: George G. <g.g...@ge...> - 2012-08-30 15:02:53
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Hi Gerhard, the error you are getting is due to the lack of the pato import. Without being 100% sure, I suspect it has nothing to do with the new OBO format. Couple of things you could do to solve this: 1. Import PATO as a separate ontology - this should solved the error you are getting, 2. If you do not want to import PATO - when you try to load the ontology click on the advance option and select the "Avoid dangling references" option. This would stop oboedit complaining about the missing PATO terms. Please let me know if this works for you. Best wishes, George On 30/08/2012 11:45, Gerhard Mayer wrote: > Hallo Mr. Gkoutos, > > I'm maintaining the psi-ms.ontology > (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). > > Since the last release (29:08:2012) of the unit.obo file I get the > following errors when I try to load my ontology by OBO-Edit 2.2: > > Load Error, line 547 48 unrecognized parent terms: > line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) > org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) > org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) > org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) > org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) > org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) > org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) > > > I saw that in former versions of the unit ontology there was the import statement > import: http://purl.obolibrary.org/obo/pato.obo > which is now missing resp. replaced by > ontology: uo > ontology: pato > > I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) > ontology: xyz > was introduced as a new docuemnt header tag. > > But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. > > In addition you specified the old 1.2 format in your unit.obo file: > format-version: 1.2 > which should be changed to > format-version: 1.4 > in case you want to use the new format. > > Best Regards, > Gerhard > |
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From: Matthew C. <mat...@gm...> - 2012-08-30 15:24:40
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Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the terms that belong to that ontology, translated to lowercase." But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... -Matt On 8/30/2012 10:02 AM, George Gkoutos wrote: > > Hi Gerhard, > > the error you are getting is due to the lack of the pato import. Without > being 100% sure, I suspect it has nothing to do with the new OBO format. > > Couple of things you could do to solve this: > > 1. Import PATO as a separate ontology - this should solved the error you > are getting, > 2. If you do not want to import PATO - when you try to load the ontology > click on the advance option and select the "Avoid dangling references" > option. This would stop oboedit complaining about the missing PATO terms. > > Please let me know if this works for you. > > Best wishes, > > George > > On 30/08/2012 11:45, Gerhard Mayer wrote: >> Hallo Mr. Gkoutos, >> >> I'm maintaining the psi-ms.ontology >> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >> >> Since the last release (29:08:2012) of the unit.obo file I get the >> following errors when I try to load my ontology by OBO-Edit 2.2: >> >> Load Error, line 547 48 unrecognized parent terms: >> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >> >> >> I saw that in former versions of the unit ontology there was the import statement >> import: http://purl.obolibrary.org/obo/pato.obo >> which is now missing resp. replaced by >> ontology: uo >> ontology: pato >> >> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >> ontology: xyz >> was introduced as a new docuemnt header tag. >> >> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >> >> In addition you specified the old 1.2 format in your unit.obo file: >> format-version: 1.2 >> which should be changed to >> format-version: 1.4 >> in case you want to use the new format. >> >> Best Regards, >> Gerhard >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit > |
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From: George G. <g.g...@ge...> - 2012-08-30 15:39:55
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On 30/08/2012 16:24, Matthew Chambers wrote: Hi Matt, your are quite right - I have now removed the ontology: pato statement. Best wishes, George > Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and > pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the > terms that belong to that ontology, translated to lowercase." > > But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same > semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to > figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers > are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... > > -Matt > > > On 8/30/2012 10:02 AM, George Gkoutos wrote: >> Hi Gerhard, >> >> the error you are getting is due to the lack of the pato import. Without >> being 100% sure, I suspect it has nothing to do with the new OBO format. >> >> Couple of things you could do to solve this: >> >> 1. Import PATO as a separate ontology - this should solved the error you >> are getting, >> 2. If you do not want to import PATO - when you try to load the ontology >> click on the advance option and select the "Avoid dangling references" >> option. This would stop oboedit complaining about the missing PATO terms. >> >> Please let me know if this works for you. >> >> Best wishes, >> >> George >> >> On 30/08/2012 11:45, Gerhard Mayer wrote: >>> Hallo Mr. Gkoutos, >>> >>> I'm maintaining the psi-ms.ontology >>> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >>> >>> Since the last release (29:08:2012) of the unit.obo file I get the >>> following errors when I try to load my ontology by OBO-Edit 2.2: >>> >>> Load Error, line 547 48 unrecognized parent terms: >>> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >>> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >>> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >>> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >>> >>> >>> I saw that in former versions of the unit ontology there was the import statement >>> import: http://purl.obolibrary.org/obo/pato.obo >>> which is now missing resp. replaced by >>> ontology: uo >>> ontology: pato >>> >>> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >>> ontology: xyz >>> was introduced as a new docuemnt header tag. >>> >>> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >>> >>> In addition you specified the old 1.2 format in your unit.obo file: >>> format-version: 1.2 >>> which should be changed to >>> format-version: 1.4 >>> in case you want to use the new format. >>> >>> Best Regards, >>> Gerhard >>> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Obo-unit mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-unit >> > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit |
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From: Chris M. <cjm...@lb...> - 2012-08-30 16:37:29
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imports are unfortunately not well supported by obo-edit. OWL is best for working with multiple ontologies. Oort can be used to generate versions of ontologies that have subsets of other ontologies merged in. UO should be released this way - can you do this George? On Aug 30, 2012, at 8:24 AM, Matthew Chambers wrote: > Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and > pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the > terms that belong to that ontology, translated to lowercase." > > But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same > semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to > figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers > are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... > > -Matt > > > On 8/30/2012 10:02 AM, George Gkoutos wrote: >> >> Hi Gerhard, >> >> the error you are getting is due to the lack of the pato import. Without >> being 100% sure, I suspect it has nothing to do with the new OBO format. >> >> Couple of things you could do to solve this: >> >> 1. Import PATO as a separate ontology - this should solved the error you >> are getting, >> 2. If you do not want to import PATO - when you try to load the ontology >> click on the advance option and select the "Avoid dangling references" >> option. This would stop oboedit complaining about the missing PATO terms. >> >> Please let me know if this works for you. >> >> Best wishes, >> >> George >> >> On 30/08/2012 11:45, Gerhard Mayer wrote: >>> Hallo Mr. Gkoutos, >>> >>> I'm maintaining the psi-ms.ontology >>> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >>> >>> Since the last release (29:08:2012) of the unit.obo file I get the >>> following errors when I try to load my ontology by OBO-Edit 2.2: >>> >>> Load Error, line 547 48 unrecognized parent terms: >>> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >>> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >>> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >>> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >>> >>> >>> I saw that in former versions of the unit ontology there was the import statement >>> import: http://purl.obolibrary.org/obo/pato.obo >>> which is now missing resp. replaced by >>> ontology: uo >>> ontology: pato >>> >>> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >>> ontology: xyz >>> was introduced as a new docuemnt header tag. >>> >>> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >>> >>> In addition you specified the old 1.2 format in your unit.obo file: >>> format-version: 1.2 >>> which should be changed to >>> format-version: 1.4 >>> in case you want to use the new format. >>> >>> Best Regards, >>> Gerhard >>> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Obo-unit mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-unit >> > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit |
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From: Chris M. <cjm...@lb...> - 2012-08-30 16:35:56
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On Aug 30, 2012, at 3:45 AM, Gerhard Mayer wrote: > But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. > > In addition you specified the old 1.2 format in your unit.obo file: > format-version: 1.2 > which should be changed to > format-version: 1.4 > in case you want to use the new format. > > Best Regards, > Gerhard Hi Gerhard The story is more complex than that. Every oboformat 1.2 ontology should be a valid 1.4 ontology. There is no formal spec for 1.2, only a rough guide. There is a formal spec for 1.4, and although some aspects of the mapping to owl have the potential to change, the 1.4 formal spec should be regarded as the canonical way to interpret any obo format file. See http://oboformat.org Are you on the obo-format list? I think it's important to have a representative of PSI-MOD there. |
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