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[bioontology-support] problem with CHDWiki ontology

Ray Fergerson ray.fergerson at stanford.edu
Fri Jun 7 17:28:40 PDT 2013


Babis,

You have nailed the problem. BioPortal does not currently support the
handling of blank nodes.

I will take care of deleting the old versions. This appears to be a gap in
our toolset...

Ray

-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
cmoschop
Sent: Tuesday, June 04, 2013 7:36 AM
To: Ray Fergerson
Cc: support at bioontology.org
Subject: Re: [bioontology-support] problem with CHDWiki ontology


Hi Ray,

thanks again for your valuable help. i created the ontology without the
protege and actually these kind of problems solved. however, i still can
not see attributes that are inserted through blank nodes. is bioportal
supporting these kind of relationships? also, is there a way to delete the
previous versions of our ontology as they do not show any different than
the last one (except the technical problems they had).

once again, thank you for your prompt answers and i really apologize for
bombarding you with emails. i really hope this will be the last one :).

regards
babis



On 2013.05.31 20:43, Ray Fergerson wrote:
> 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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