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[bioontology-support] Minor load issues with EFO

Timothy Redmond tredmond at stanford.edu
Thu Aug 15 21:07:15 PDT 2013


On 08/15/2013 01:38 PM, Ray Fergerson wrote:
> James,
>
> Would it be possible to just add the definitions for these concepts? That
> is probably the fastest way to deal with this problem.

That should work.  I tried it and the end result (after post-processing) 
looked right in Protege 3.  I did some checking into this ontology and 
there are other missing declarations that might possibly lead to other 
anomalies.

I was wondering how this file came about.  At the bottom there is a line 
that says:

     <!-- Generated by the OWL API (version 3.2.3.1824) http://owlapi.sourceforge.net -->


Normally files generated by the owl api should not be missing 
declarations although there is a flag that will allow it to write files 
that are missing declarations.  There is a flag though (something like 
addMissingDeclarations=false) that will allow this. Did this file get 
edited by a text-editor after the OWL api processed it?

-Timothy


>
> Ray
>
> -----Original Message-----
> From: Timothy Redmond [mailto:tredmond at stanford.edu]
> Sent: Thursday, August 15, 2013 7:38 AM
> To: James Malone
> Cc: Ray Fergerson; support at bioontology.org
> Subject: Re: [bioontology-support] Minor load issues with EFO
>
> On 08/15/2013 03:16 AM, James Malone wrote:
>> Hi,
>>
>> Any updates on this?
> Sorry - I have been a bit slow picking this up.  I will have to do some
> more research but my first observation is that these two resources seem
> to be both missing their declarations.   This makes parsing these
> ontoloigies more difficult and may account for Protege confusing them with
> classes.
>
> In OWL 2, missing declarations put an ontology into OWL 2 full.  The
> specification of an OWL 2 rdf parser is somewhat strict about these types
> of problems putting the onus on the ontology developer to make sure
> everything is properly declared.
>
> I will look at this some more later today.
>
> -Timothy
>
>> Cheers,
>>
>> James
>>
>> On 10/08/2013 01:43, Ray Fergerson wrote:
>>> Forwarding this to our Protégé expert, Tim. He has explained to me
>>> before what causes this but I can't seem to remember the explanation
>>> for more than 15 minutes. Perhaps if he documents it here I can come
>>> back to it...
>>>
>>> Tim?
>>>
>>> Ray
>>>
>>> -----Original Message-----
>>> From: bioontology-support-bounces at lists.stanford.edu
>>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
>>> James Malone
>>> Sent: Friday, August 09, 2013 1:40 AM
>>> To: support at bioontology.org Support
>>> Subject: [bioontology-support] Minor load issues with EFO
>>>
>>> Hi,
>>>
>>> There seems to be a bit of weirdness in the EFO hierarchy as visible
>>> in BioPortal. At top level, two additional classes are showing
>>> 'expand expression to' (from IAO) and 'has_scope' (from OBO in OWL)
>>> which are both annotation properties. Not sure whey they are showing
>>> there.
>>>
>>> Thanks,
>>>
>>> James
>>>
>>> --
>>> Blog: http://jamesmaloneebi.blogspot.co.uk/
>>> Twitter: https://twitter.com/jamesmalone
>>>
>>> European Bioinformatics Institute,
>>> Wellcome Trust Genome Campus,
>>> Cambridge, CB10 1SD,
>>> United Kingdom
>>> Tel: + 44 (0) 1223 494 676
>>> Fax: + 44 (0) 1223 494 468
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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