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[bioontology-support] Minor load issues with EFO

Timothy Redmond tredmond at stanford.edu
Thu Aug 15 07:38:11 PDT 2013


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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