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[bioontology-support] Minor load issues with EFO

Timothy Redmond tredmond at stanford.edu
Fri Aug 16 09:51:50 PDT 2013


On 8/16/13 1:21 AM, James Malone wrote:
> 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.

Ok - so this is not too important but I am still interested in tracking 
it down.  Are you using the vanilla Protege from Stanford or are you 
using a different version?  If you are using a vanilla version from 
Stanford, what build are you using?

Thanks,

-Timothy

>
> 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
>>
>



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