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[bioontology-support] problem with CHDWiki ontology

Ray Fergerson ray.fergerson at stanford.edu
Fri May 31 11:43:28 PDT 2013


Bibis,

Sorry, I didn't cover the entire issue in my previous response.

Previously your ontology would not display at all in BioPortal. Trying to 
navigate terms in the UI resulted in a hang on every term. This problem has 
been fixed.

BioPortal does not currently support restrictions. Thus clauses like 
"involved_with some X" are effectively ignored. That is why you are not 
seeing what you expect to see. We are reconsidering this policy in the new 
backend system that we are working on but, even there, the problem is not so 
simple since everything is stored as triples. It is likely to not be 
addressed in the first release.

Ray


-----Original Message-----
From: cmoschop [mailto:Charalampos.Moschopoulos at esat.kuleuven.be]
Sent: Friday, May 31, 2013 6:43 AM
To: Ray Fergerson
Cc: 'cmoschop'; support at bioontology.org
Subject: RE: [bioontology-support] problem with CHDWiki ontology

Dear Ray and bioportal support team,

first of all i would like to thank you for your so far help.
I uploaded a new version of our CHDWiki ontology but the problems are still 
present.
I noticed that only the Annotation properties of the rdfs schema are 
recognized by bioportal.
After checking other ontologies, hosted by bioportal (for example HUGO), i 
thought that the problem is the base prefix so i followed the HUGO example. 
However, still at the bioportl only the Annotation and Object properties 
under rdfs schema are been shown.
could you inform me about what i might do wrong?

thanks in advance
babis



On 2013.05.30 00:45, Ray Fergerson wrote:
> This is working now in the UI.
>
> Ray
>
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
> cmoschop
> Sent: Friday, May 24, 2013 6:38 AM
> To: support at bioontology.org
> Subject: [bioontology-support] problem with CHDWiki ontology
>
> Dear Sirs,
> I recently submitted an ontology in Bioportal, called CHDWiki, which
> was created using Protege and saved at OWL-Manchester syntax format.
> when i tried to navigate to our ontology, i realized that only the
> is_a relationships have been preserved. Relationships between the
> ontology classes have been disappeared (involved_in and
> connected_with).
> Also, i couldn't query the data through http://sparql.bioontology.org.
> could you inform me what i did wrong? should i submit the ontology
> under a different format?
>
> thank you in advance!
>
> best regards
> Charalampos Moschopoulos
>
> --
> Charalampos Moschopoulos
> Post Doctoral Researcher - Bioinformatics Dept. Electrical Engineering
> SCD/SISTA K.U. Leuven Belgium Tel + 32 16 32 86 47 Fax +32 16 32 19
> 70
> moschopoulos.wordpress.com
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-- 
Charalampos Moschopoulos
Post Doctoral Researcher - Bioinformatics
Dept. Electrical Engineering SCD/SISTA
K.U. Leuven
Belgium
Tel + 32 16 32 86 47
Fax +32 16 32 19 70
moschopoulos.wordpress.com


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