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[bioontology-support] Minor load issues with EFO

Ray Fergerson ray.fergerson at stanford.edu
Thu Aug 15 13:38:29 PDT 2013


James,

Would it be possible to just add the definitions for these concepts? That
is probably the fastest way to deal with this problem.

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
>>
>> _______________________________________________
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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>



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