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[bioontology-support] CCO and SIO

Ray Fergerson rayferg at stanford.edu
Thu Oct 29 14:44:53 PDT 2015


I agree that an OWL file is probably the way to go. Note that loading the file into Virtuoso just proves that it is valid RDF. We use the OWLAPI parser which requires the file to be valid OWL, before it goes into our triplestore. If you generate OWL yourself you might try loading it with this parser before trying to load it into bioportal.

Ray

From: Vladimir Mironov [mailto:vladimir.n.mironov at gmail.com]
Sent: Thursday, October 29, 2015 1:45 AM
To: Michel Dumontier
Cc: Ray Fergerson; Michel Dumontier; support
Subject: Re: CCO and SIO

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<mailto: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<mailto: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<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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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