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[bioontology-support] New EFO file

James Malone malone at ebi.ac.uk
Tue Sep 8 04:41:10 PDT 2009


Hi Trish,

Ah yes the efo prefix. I was assuming it's because the code in BioPortal 
is turning the first part of the namespace into its short version using 
this:

xmlns:efo="http://www.ebi.ac.uk/efo/"

This is not how it is in the OWL file, we use the full URI for example:

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0001595">

Actually I would really prefer the efo:EFO_00000001 not to be displayed 
this way because it makes querying impossible. For one, because you 
can't access the namespace declerations you can't resolve what "efo:" 
actually means in the browser. I would much rather have either the full 
URI or just the fragment after the namespace:

http://www.ebi.ac.uk/efo/EFO_0001595
or
EFO_0001595

Any chance of this being possible? :)

Cheers,

James



Trish Whetzel wrote:
> Hi James,
>
> The new version has been loaded 
> (http://bioportal.bioontology.org/visualize/40583/), however after 
> reviewing I noticed that the term identifiers have the extra 'efo' 
> prefix that has been present in a few earlier versions.
>
> Also, what is the BioPortalImporter v1.0 as noted in the definition 
> editor field for some terms, e.g. 
> http://bioportal.bioontology.org/visualize/40583/efo%3AEFO_0001367?
>
> Trish
>
>
> On Sep 4, 2009, at 9:04 AM, James Malone wrote:
>
>> Dear BioPortal,
>>
>> We have our monthly EFO release ready for uploading to BioPortal 
>> please!  The file is available here 
>> http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl 
>>
>>
>> Many thanks in advance.
>>
>> James
>>
>> -- 
>> European Bioinformatics Institute, Wellcome Trust Genome Campus, 
>> Hinxton, Cambridge, CB10 1SD, United Kingdom
>> Tel: + 44 (0) 1223 494 676
>> Fax: + 44 (0) 1223 492 468
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


-- 
European Bioinformatics Institute, 
Wellcome Trust Genome Campus, 
Hinxton, 
Cambridge, CB10 1SD, 
United Kingdom
Tel: + 44 (0) 1223 494 676
Fax: + 44 (0) 1223 492 468 




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