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[bioontology-support] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Mon Feb 2 15:05:18 PST 2009


Hi Alan,

Since the import processing is based on Protégé itself that question would
be best for Tim or Tania.

Trish


>-----Original Message-----
>From: Alan Ruttenberg [mailto:alanruttenberg at gmail.com]
>Sent: Monday, February 02, 2009 2:43 PM
>To: Trish Whetzel
>Cc: Melanie Courtot; bioontology-support at mailman.stanford.edu
>Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display
>
>Hi Trish,
>
>I'm doing some further investigation. Some of the duplication is being
>generated via imports. Is there a description of the imports
>processing that bioportal is doing that I could get?
>
>-Alan
>
>On Mon, Feb 2, 2009 at 1:33 PM, Trish Whetzel <whetzel at stanford.edu>
>wrote:
>> 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 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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