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[bioontology-support] Fwd: Problem with Bioportal display

Alan Ruttenberg alanruttenberg at gmail.com
Mon Feb 2 13:14:04 PST 2009


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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