Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] CCO and SIO

Vladimir Mironov vladimir.n.mironov at gmail.com
Thu Oct 29 01:44:38 PDT 2015


HI all,

the point is that there are several ID spaces used in the CCO, both for
Terms and TypeDefs. I don't see how one can specify the mapping for each
individual Term/TypDef in OBO 1.4.
In this situation it might be more productive to concentrate on solving the
problem with uploading an OWL version of the CCO. My previous attempts to
upload to BioPortal failed even though I could successfully upload into
Virtuoso.

Ray, could not this be due to the size of the OWL file? Some time ago when
you changed the software I experienced this type of problem with OBO files
and eventually that was solved. I can generate an OWL file for the latest
version of the CCO and send it to you, just let me know.

Cheers,
Vladimir


On 27 October 2015 at 19:57, Michel Dumontier <michel.dumontier at gmail.com>
wrote:

> ok, looks like there is an 'idspace' tag that you can use to map a local
> id to a uri
>
>
> http://owlcollab.github.io/oboformat/doc/obo-syntax.html
>
> *idspace(IDPrefix URIPrefix)*
>
> 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 Tue, Oct 27, 2015 at 7:07 PM, Ray Fergerson <rayferg at stanford.edu>
> wrote:
>
>> Not that I know of but I am hardly the expert. I had a look at the CCO
>> OBO file and there was no obvious place for it to be specified.
>>
>>
>>
>> Ray
>>
>>
>>
>> *From:* Michel Dumontier [mailto:michel.dumontier at stanford.edu]
>> *Sent:* Tuesday, October 27, 2015 10:56 AM
>> *To:* Ray Fergerson
>> *Cc:* Michel Dumontier; support; Vladimir Mironov
>>
>> *Subject:* Re: CCO and SIO
>>
>>
>>
>> is there no way to specify the uri prefix in obo?
>>
>>
>>
>> m
>>
>> On Tuesday, October 27, 2015, Ray Fergerson <rayferg at stanford.edu> wrote:
>>
>> I believe that any URI’s are lost in the conversion to OBO.  The ids for
>> terms in obo are not URI’s but are instead of the format:
>>
>>
>>
>> id: CCO:0000001
>>
>>
>>
>> Since there are no URI’s, we generate them.
>>
>>
>>
>> If you upload and OWL file we should respect the URI’s that are in the
>> file.
>>
>>
>>
>> Ray
>>
>>
>>
>> *From:* bioontology-support [mailto:
>> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *Michel
>> Dumontier
>> *Sent:* Tuesday, October 27, 2015 9:45 AM
>> *To:* support
>> *Cc:* Vladimir Mironov
>> *Subject:* [bioontology-support] Fwd: CCO and SIO
>>
>>
>>
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Michel Dumontier, PhD
>> Associate Professor of Medicine (Biomedical Informatics)
>> Stanford University
>> http://dumontierlab.com
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20151029/154f3e45/attachment-0001.html>


More information about the bioontology-support mailing list