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[bioontology-support] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Mon Feb 2 12:40:16 PST 2009


I thought that you were going to upload a file that did not have the
replicated information?

Trish


>-----Original Message-----
>From: Alan Ruttenberg [mailto:alanruttenberg at gmail.com]
>Sent: Monday, February 02, 2009 12:03 PM
>To: Trish Whetzel
>Cc: Melanie Courtot; bioontology-support at mailman.stanford.edu
>Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display
>
>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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