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[bioontology-support] Fwd: CCO and SIO

Michel Dumontier michel.dumontier at stanford.edu
Tue Oct 27 09:45:14 PDT 2015


Hi team,
  There's a problem in getting the right URIs for SIO terms included in
Vladimir's CCO ontology. The ontology is represented as an OBO file, but
for whatever reason some default purl namespace is being assigned to the
terms.  Could you investigate?

m.

Michel Dumontier, PhD
Associate Professor of Medicine (Biomedical Informatics)
Stanford University
http://dumontierlab.com

---------- Forwarded message ----------
From: Vladimir Mironov <vladimir.n.mironov at gmail.com>
Date: Tue, Oct 27, 2015 at 10:22 AM
Subject: Re: CCO and SIO
To: Michel Dumontier <michel.dumontier at gmail.com>


HI Michel,

some clarification on the situation with the CCO.
The problem with the URIs is a long standing issue and it lies actually on
BioPortal's side. All the URIs in the CCO have always been correct in my
RDF files. However, when I upload something to BioPortal in the OBO format
they assign OBO foundry URIs to everything without any respect to the
source.
I don't know how to tackle this problem. As a way out once I tried to
upload an OWL file (validated in Virtuoso) without avail. I suspect this
has something to do with the size of the file, I had a similar problem even
with OBO ontologies after BioPortal chaged the software a while ago (it
took them quite some time to trace down the problem).
The message is that unless this problem is solved it won't be possible to
have correct CCO URIs in BioPortal.
Do you have any suggestions?

Cheers,
Vladimir

On 21 October 2015 at 17:23, Michel Dumontier <michel.dumontier at gmail.com>
wrote:

> sure thanks :)
>
> m.
>
> Michel Dumontier
> Associate Professor of Medicine (Biomedical Informatics), Stanford
> University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
> http://dumontierlab.com
>
> On Wed, Oct 21, 2015 at 5:23 PM, Vladimir Mironov <
> vladimir.n.mironov at gmail.com> wrote:
>
>> Of course, this may be done even earlier than the upload to virtuoso.
>> If you wish I can drop you a line when this is done.
>> V.
>>
>> On 21 October 2015 at 11:15, Michel Dumontier <michel.dumontier at gmail.com
>> > wrote:
>>
>>> thanks!!!
>>>   so this will propagate to bioportal right?
>>> m.
>>>
>>> Michel Dumontier
>>> Associate Professor of Medicine (Biomedical Informatics), Stanford
>>> University
>>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>>> Group
>>> http://dumontierlab.com
>>>
>>> On Wed, Oct 21, 2015 at 11:04 AM, Vladimir Mironov <
>>> vladimir.n.mironov at gmail.com> wrote:
>>>
>>>> HI Michel,
>>>>
>>>> thanks for your attention.
>>>> I noticed this problem before and now I have a new corrected version of
>>>> the CCO, I just need to upload it into Virtuoso.
>>>> Cheers
>>>>
>>>> On 20 October 2015 at 10:10, Michel Dumontier <
>>>> michel.dumontier at gmail.com> wrote:
>>>>
>>>>> Hi Vladimir,
>>>>>  I just discovered that you are not correctly using the SIO URIs in
>>>>> the CCO -
>>>>>
>>>>> http://purl.obolibrary.org/obo/SIO_000000
>>>>>
>>>>> should be
>>>>>
>>>>>
>>>>> http://semanticscience.org/resource/SIO_000000
>>>>> m.
>>>>>
>>>>> Michel Dumontier
>>>>> Associate Professor of Medicine (Biomedical Informatics), Stanford
>>>>> University
>>>>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>>>>> Group
>>>>> http://dumontierlab.com
>>>>>
>>>>
>>>>
>>>
>>
>
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