Re: [OBO-Edit Working Group] problem to open OBO format ontologies using OBO-editor

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Hi Jie and Melissa,

 From http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page there 
are four versions of Uberon available in OBO and OWL from the table:

main: the full ontology with externally-referencing axioms removed 
(pre-reasoned)
basic: a simplified version of the ontology, with only is_a, part_of and 
develops_from relationships (pre-reasoned)
merged: full ontology plus externally referencing axioms plus merged in 
subset of GO, CL, PRO, CHEBI and NCBITaxon (pre-reasoned)
core: full ontology plus externally referencing axioms left "dangling" 
(not pre-reasoned)

Of the OBO versions, "main," "basic," and "merged" all loaded fine in 
OBO-Edit 2.3-b2, but "core" had an error:

Load Error, line 3979 Found unexpected scope identifier SENSU

This is not a dangling reference error.

Not sure which Uberon you need, but hopefully one of the working files 
will work for you,

Best regards,

Alex

On 11/2/12 10:07 AM, Melissa Haendel wrote:
> Jie,
> I am able to load uberon in obo edit just fine from
> http://obo.svn.sourceforge.net/svnroot/obo/uberon/trunk/uberon.obo
>
> are you sure you checked the dangling references box?
>
> This version of obi also opens:
> http://www.berkeleybop.org/ontologies/obo-all/obi/obi.obo
> though it is somewhat hard to browse as the external references are 
> not included.
>
> I can help you sometime soon if you like.
> Cheers
> Melissa
>
> On Nov 2, 2012, at 3:03 AM, Dr Midori A. Harris wrote:
>
>> Dear Jie,
>>
>> Unfortunately I can't help with anything specific in OBI, or with which
>> versions of UBERON are available from various links.
>>
>> I think you might be able to find some assistance via tho OBO-idscuss
>> mailing list (<Obo...@li... 
>> <mailto:Obo...@li...>> or see
>> https://lists.sourceforge.net/lists/listinfo/obo-discuss).
>>
>> Good luck!
>>
>> Midori
>>
>> On Thu, 1 Nov 2012, Jie Zheng wrote:
>>
>>> Dear Midori,
>>>
>>> Sorry to bother you again.
>>>
>>> I found the obi.obo on OBO foundry website is an old version. I 
>>> tried to load
>>> latest release version of OBO format OBI which can be found on:
>>> http://www.berkeleybop.org/ontologies/obi.obo (redirected from the link
>>> http://purl.obolibrary.org/obo/obi.obo).
>>>
>>> This obo format OBI is generated using Oort tool during OBI release 
>>> process.
>>>
>>> I got following error when I tried to load it to OBO editor with 
>>> checking
>>> 'Allow dangling references':
>>> *Load Error, line 70*
>>> /Attempted to set comment of object null which does not support 
>>> comments./
>>>
>>> *
>>> org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1451)
>>>
>>> *
>>> org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1443)
>>>
>>> * org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:407)
>>> * 
>>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
>>>
>>> * 
>>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72)
>>>
>>> * 
>>> 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)
>>>
>>>
>>> How can I fix it?
>>>
>>> Thanks a lot,
>>>
>>> Jie
>>>
>>>
>>> On 11/1/2012 4:34 PM, Jie Zheng wrote:
>>>> Dear Midori,
>>>>
>>>> Thanks for checking it.
>>>>
>>>> I am a newbie of OBO editor. So, it is me a while to find out how 
>>>> to set
>>>> allow dangling references. Now, loading OBI worked. Loading 
>>>> uberon.obo that
>>>> I downloaded from
>>>> http://www.obofoundry.org/cgi-bin/detail.cgi?id=uberon
>>>> still did not work.
>>>>
>>>> However, loading it from
>>>> http://obo.svn.sourceforge.net/svnroot/obo/uberon/trunk/uberon.obo 
>>>> works no
>>>> matter I checked 'Allow dangling references' or not.
>>>>
>>>> Thanks for you help.
>>>>
>>>> Jie
>>>>
>>>>
>>>> On 11/1/2012 6:17 AM, Dr Midori A. Harris wrote:
>>>>> Dear Jie,
>>>>>
>>>>> I tried loading the OBO format version of OBI available at
>>>>> http://www.berkeleybop.org/ontologies/obo-all/obi/obi.obo, and I 
>>>>> found
>>>>> that it loads if I check the "Allow dangling references" option. 
>>>>> You'll
>>>>> see it in the lower left corner of the Advanced load dialog box.
>>>>>
>>>>> The UBERON file from
>>>>> http://obo.svn.sourceforge.net/svnroot/obo/uberon/trunk/uberon.obo 
>>>>> loaded
>>>>> for me, so perhaps your problem was transient.
>>>>>
>>>>> The missing type in cl.obo should be reported to the Cell Type 
>>>>> Ontology
>>>>> editors, using either of the trackers linked here:
>>>>> http://cellontology.org/?q=issues
>>>>>
>>>>> (Note: I don't work on any of these three ontologies; I just use 
>>>>> OBO-Edit
>>>>> with a different ontology that also needs the "allow dangling 
>>>>> references"
>>>>> option, so I thought of it.)
>>>>>
>>>>> Midori
>>>>>
>>>>> On Wed, 31 Oct 2012, Jie Zheng wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I tried to open OBO format OBI (generated using Oort tool) using
>>>>>> OBO-editor (window version 2.2 and 2.3). I got following errors:
>>>>>> Load Error, line -1 Assigned non-existant range
>>>>>> IDhttp://purl.obolibrary.org/obo/NCBITaxon_9606|http://purl.obolibrary.org/obo/OBI_0000245 
>>>>>> <IDhttp://purl.obolibrary.org/obo/NCBITaxon_9606%7Chttp://purl.obolibrary.org/obo/OBI_0000245> 
>>>>>>
>>>>>> to term OBI:0000304
>>>>>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1369) 
>>>>>>
>>>>>> 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) 
>>>>>>
>>>>>>
>>>>>> How can I fix it?
>>>>>>
>>>>>> I also tried other obo format ontologies downloaded
>>>>>> fromhttp://www.obofoundry.org/  website.
>>>>>>
>>>>>> For Uberon ontology, I got this error:
>>>>>> Load Error, line 1 Expected :.
>>>>>> org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1451) 
>>>>>>
>>>>>> org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1443) 
>>>>>>
>>>>>> org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:330)
>>>>>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48) 
>>>>>>
>>>>>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72) 
>>>>>>
>>>>>> 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) 
>>>>>>
>>>>>>
>>>>>> For Cell type ontology (cl.obo), I got this error message:
>>>>>> Unrecognized type derives_from
>>>>>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1295) 
>>>>>>
>>>>>> 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) 
>>>>>>
>>>>>>
>>>>>> Could you please check it?
>>>>>>
>>>>>> Thanks a lot.
>>>>>>
>>>>>> Jie
>>>>>>
>>>>>>
>>>>>>
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>>>>>> _______________________________________________
>>>>>> Geneontology-oboedit-working-group mailing list
>>>>>> Gen...@li... 
>>>>>> <mailto:Gen...@li...>
>>>>>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group 
>>>>>>
>>>>>>
>>>>>
>>>>> Midori A. Harris, PhD
>>>>> Database Curator, PomBase
>>>>> Department of Biochemistry
>>>>> University of Cambridge
>>>>> Cambridge, UK
>>>>> ma...@ca... <mailto:ma...@ca...>
>>>>
>>>
>>>
>>
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>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
>
> *Dr. Melissa Haendel
> *
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/
> Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> ha...@oh... <mailto:ha...@oh...>
> skype: melissa.haendel
> 503-407-5970
>
>
>
>
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Re: [OBO-Edit Working Group] problem to open OBO format ontologies using OBO-editor

The DEPRECATED legacy location of the GO, see http://geneontology.org

Re: [OBO-Edit Working Group] problem to open OBO format ontologies using OBO-editor