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[bioontology-support] Fwd: Problem with Bioportal display

Alan Ruttenberg alanruttenberg at gmail.com
Mon Feb 2 14:42:41 PST 2009


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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