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[bioontology-support] Fwd: parsing error- TO

Trish Whetzel whetzel at stanford.edu
Mon May 7 10:29:28 PDT 2012


Hi Laurel, 

Paul has fixed the issue with TO being listed with the status of parsing error. I believe this was a consequence of an issue with a release pushed out last Thursday. Before this time, it looks like the automatic pull for TO was working correctly after the URL change and new versions of TO are currently set to be loaded automatically via the specified URL.

Trish 


On May 7, 2012, at 10:11 AM, Trish Whetzel wrote:

> 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>
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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