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[bioontology-support] CCO and SIO

Michel Dumontier michel.dumontier at gmail.com
Tue Oct 27 11:57:33 PDT 2015


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
>
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