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[bioontology-support] Minor load issues with EFO

James Malone malone at ebi.ac.uk
Fri Aug 16 01:21:11 PDT 2013


Hi Tim,

We've been doing some programmatic imports so they've been run through 
the owlapi, however these files are read into Protege 4 for release and 
spat out again. I'll check the definitions for these properties though 
and make sure they're added, thanks for the help.

James


On 16/08/2013 05:07, Timothy Redmond wrote:
> 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
>

-- 
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



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