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[bioontology-support] problem with CHDWiki ontology

cmoschop Charalampos.Moschopoulos at
Tue Jun 4 07:36:15 PDT 2013

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 


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]
> Sent: Friday, May 31, 2013 6:43 AM
> To: Ray Fergerson
> Cc: 'cmoschop'; support at
> 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
>> [mailto:bioontology-support-bounces at] On Behalf Of
>> cmoschop
>> Sent: Friday, May 24, 2013 6:38 AM
>> To: support at
>> 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 
>> 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
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at

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

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