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[bioontology-support] [BioPortal] Evidence codes Parsing Failed

Marcus Chibucos mchibucos at gmail.com
Fri Aug 31 13:23:20 PDT 2012


Hi Paul,

Excellent! Thank you for your quick turnaround on the issue. I figured 
it was something relatively simple, but I was at a loss as to what it 
was. Thanks for explaining.

Cheers,
Marcus


On 08/31/2012 04:16 PM, Paul R Alexander wrote:
> Marcus,
>
> The URL you provided for us to pull the ontology from was an HTML view 
> of the OBO file. We would need a link directly to the OBO file in 
> order to parse the ontology properly. When you are looking at the HTML 
> view, there is a link on the page that says "View raw file". The link 
> leads here:
> http://evidenceontology.googlecode.com/svn/trunk/eco.obo
>
> I submitted this URL as a new version of the ontology. It should get 
> pulled and parsed in the next few hours.
>
> Let me know if you have any questions.
>
> Paul
>
>
> On 8/31/12 7:13 AM, Marcus Chibucos wrote:
>> Hello BioPortal,
>>
>> I am the developer of ECO, the Evidence Ontology. The other night I 
>> modified some of the metadata here: 
>> http://bioportal.bioontology.org/ontologies/1012
>>
>> Since then, I have been getting a periodic email from BioPortal 
>> noting a parsing failure. I am not sure why, but perhaps if I 
>> explained my goal, you would be so kind as to help me get ECO back 
>> online at BioPortal...
>>
>> Not long ago we gave ECO its own development site, at Google Code 
>> rather than SourceForge. My goal was for BioPortal to pull the 
>> ontology from now on from here: 
>> http://code.google.com/p/evidenceontology/source/browse/trunk/eco.obo
>> So I changed the "ontology location" on the BioPortal metadata page 
>> to that. Is this not correct?
>>
>> We also have a subversion repository checkout, with instructions for 
>> checking out here: 
>> http://code.google.com/p/evidenceontology/source/checkout
>>
>> I would be grateful for any help you could offer in suggesting proper 
>> settings so that BioPortal parses ECO from our Google Code site.
>>
>> Many thanks,
>> Marcus
>>
>> Marcus Chibucos
>> Evidence Ontology (ECO)
>> Institute for Genome Sciences
>> University of Maryland School of Medicine
>> Baltimore, Maryland 21201
>> (410) 706-0885
>> mchibucos at som.umaryland.edu
>>
>>
>> On 08/31/2012 12:04 AM, support at bioontology.org wrote:
>>> Evidence codes parsing failed.
>>>
>>> The BioPortal team is investigating the issue.
>>>
>>> Please contact support at bioontology.org if you have questions.
>>>
>>> Thank you,
>>> The BioPortal Team 
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>



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