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

Paul R Alexander palexander at stanford.edu
Fri Aug 31 13:16:59 PDT 2012


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 
>
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> bioontology-support at lists.stanford.edu
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