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[bioontology-support] Fwd: Problem with Bioportal display

Alan Ruttenberg alanruttenberg at gmail.com
Mon Feb 2 12:02:40 PST 2009


It shouldn't write "definition" more than once no matter how many times one has

OBI_XXXXX rdfs:label "definition".

If I write


OBI_XXXXX rdfs:label "definition".
OBI_XXXXX rdfs:label "definition".
OBI_XXXXX rdfs:label "definition".
OBI_XXXXX rdfs:label "definition".

There is still really only one triple.
-Alan


On Mon, Feb 2, 2009 at 12:01 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> Hmm, buggy in what way? Is {definition, defintion} still displayed with the
> added annotation files removed?
>
> Trish
>
>
>>-----Original Message-----
>>From: Alan Ruttenberg [mailto:alanruttenberg at gmail.com]
>>Sent: Monday, February 02, 2009 11:59 AM
>>To: Trish Whetzel
>>Cc: Melanie Courtot; bioontology-support at mailman.stanford.edu
>>Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display
>>
>>We can, however the behavior is still buggy in P3. An RDF graph is a
>>set of triples, not a multi-set.
>>Of course the behavior of P4 is *also* buggy. Sigh...
>>-Alan
>>
>>http://en.wikipedia.org/wiki/Multiset
>>
>>On Mon, Feb 2, 2009 at 11:35 AM, Trish Whetzel <whetzel at stanford.edu>
>>wrote:
>>> Hi Alan and Melanie,
>>>
>>>
>>>
>>> Can a new OBI file be uploaded that does not have the definitions
>>added to
>>> all the files, ie the change that Alan made for p4? BioPortal uses
>>Protégé
>>> 3.4.
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Trish
>>>
>>>
>>>
>>>
>>>
>>> From: bioontology-support-bounces at lists.stanford.edu
>>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
>>Trish
>>> Whetzel
>>> Sent: Saturday, January 31, 2009 9:56 AM
>>> To: bioontology-support at lists.stanford.edu
>>> Subject: [bioontology-support] Fwd: Problem with Bioportal display
>>> Begin forwarded message:
>>>
>>> From: Alan Ruttenberg <alanruttenberg at gmail.com>
>>> Date: January 31, 2009 8:56:12 AM PST
>>> To: Trish Whetzel <plwhetzel at gmail.com>, Benjamin Dai
>>> <benjamin.dai at stanford.edu>
>>> Cc: Melanie Courtot <mcourtot at gmail.com>
>>> Subject: Problem with Bioportal display
>>>
>>> http://bioportal.bioontology.org/visualize/39300/IAO_0000018
>>>
>>> Note that labels are repeated.
>>> Regardless of whether the label statement is asserted in more than one
>>> file, identical triples are considered one, and so duplicate labels
>>> should never appear. In all cases, in a logical expression, only a
>>> single label should be shown. Should there be more than one, a tooltip
>>> can supply further information.
>>>
>>>
>>>
>>> I recall that annotation properties were added in duplicate/triplicate
>>in
>>> this release of OBI. In the email to the obi-devel list titled
>>Rendering
>>> Problem:
>>>
>>> Caused by me. Possible lesser of two evils. p4 doesn't like it if the
>>> annotation properties aren't defined in the file that uses them. So I
>>> added definitions to all the files. I've been debugging performance
>>> and this was done while doing so. I can get rid of them, but if it's
>>> not too much trouble I'd prefer to leave them. It's a bug that protege
>>> displays the same thing more than once though.
>>> -Alan
>>>
>>>
>>>
>>> As follow-up I have reviewed OBI in both Protégé 3.4 build 519 and
>>Protégé
>>> 4. In Protégé 4, the labels are not repeated, however in Protégé 3.4
>>they
>>> are, ie {definition, definition}. I have reported this as a bug with
>>> BioPortal (Bug #1043). Alan, did you report this on the Protégé
>>mailing
>>> list?
>>>
>>>
>
>



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