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[bioontology-support] Fwd: Problem with Bioportal display

Alan Ruttenberg alanruttenberg at gmail.com
Mon Feb 2 15:15:34 PST 2009


Ok. I see what is happening. The labels are defined in

http://purl.obofoundry.org/obo/iao/2009-01-23/iao.owl and in
http://purl.obofoundry.org/obo/iao/2009-01-23/ontology-metadata.owl

iao.owl is imported by obi.owl

So during imports, there is one label that is picked up from iao.owl
and a second (which is exactly the same) picked up by
ontology-metadata.owl. I have removed the ones in iao.owl.

However this behavior really should be fixed in protege. (Tim?)

There may be other duplications in the OBI.owl file proper - Melanie
can answer that.

-Alan

On Mon, Feb 2, 2009 at 3:05 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> 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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