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[bioontology-support] Fwd: parsing error- TO

Trish Whetzel whetzel at stanford.edu
Mon May 7 10:11:42 PDT 2012


Hi Laurel, 

I can take a first pass at reviewing this new issue. To get a few more details, are you trying to load the attached OBO format file as a new version of the Plant Trait Ontology [1] and when the file is loaded what error message is returned from BioPortal? 

Trish 

[1] http://bioportal.bioontology.org/ontologies/1037


On May 7, 2012, at 9:25 AM, Laurel Cooper wrote:

> I seem to be having ongoing problems with the TO parsing.  I have not been able to do a manual upload since Friday, so I changed it the back to doing the autoload from the url.  
> We really need to be able to have it up for today's work though, so I am attaching the obo file and hoping someone there could update it on the site,
> 
> Thanks, Laurel
> 
> On 4/26/12 11:16 AM, Trish Whetzel wrote:
>> 
>> It looks like the URL for the file location was for the html marked up version:
>> http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=markup
>> 
>> versus for the text file:
>> http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=co
>> 
>> I can update the URL if you like,
>> Trish 
>> 
>> 
>> On Apr 26, 2012, at 2:05 PM, Trish Whetzel wrote:
>> 
>>> Hi Laurel, 
>>> 
>>> I'll take a look at this.
>>> 
>>> Best, 
>>> Trish 
>>> 
>>> 
>>> On Apr 26, 2012, at 2:01 PM, Laurel Cooper wrote:
>>> 
>>>> 
>>>> 
>>>> -------- Original Message --------
>>>> Subject:	parsing error- TO
>>>> Date:	Thu, 26 Apr 2012 10:56:29 -0700
>>>> From:	Laurel Cooper <cooperl at science.oregonstate.edu>
>>>> To:	Trish Whetzel <whetzel at stanford.edu>
>>>> 
>>>> The TO parsing failed this am, do you know why?  Or maybe you an direct 
>>>> me to someone else who can help,
>>>> Thanks,
>>>> Laurel
>>>> 
>>>> -- 
>>>> **********************************************************
>>>> Laurel (Lol) Cooper, PhD
>>>> Coordinator, Plant Ontology Consortium
>>>> Dept. of Botany and Plant Pathology
>>>> Rm 3086, Cordley Hall
>>>> Oregon State University
>>>> Corvallis, OR 97331
>>>> Web: www.plantontology.org
>>>> 
>>>> Phone: 541-737-5272
>>>> Fax: 541-737-3573
>>>> Skype: cooperlol910
>>>> ***********************************************************
>>>> 
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> http://www.bioontology.org
>>> 
>>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>> 
>>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>>> 
>>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> http://www.bioontology.org
>> 
>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>> 
>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>> 
>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>> 
> 
> -- 
> **********************************************************
> Laurel (Lol) Cooper, PhD
> Coordinator, Plant Ontology Consortium
> Dept. of Botany and Plant Pathology
> Rm 3086, Cordley Hall
> Oregon State University
> Corvallis, OR 97331
> Web: www.plantontology.org
> 
> Phone: 541-737-5272
> Fax: 541-737-3573
> Skype: cooperlol910
> ***********************************************************
> <trait.obo>


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