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[bioontology-support] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Mon Feb 2 13:33:11 PST 2009


Yes, that was clear. Thanks.

On Feb 2, 2009, at 1:14 PM, Alan Ruttenberg <alanruttenberg at gmail.com>  
wrote:

> Yes, I will. I was pointing out that the current behavior (with the
> file you don't want) is incorrect. I wasn't sure whether that was
> clear. Is it?
> -Alan
>
> On Mon, Feb 2, 2009 at 12:40 PM, Trish Whetzel  
> <whetzel at stanford.edu> wrote:
>> 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 P 
>>>>>> rotégé 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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