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[bioontology-support] FW: Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Mon Feb 2 18:19:30 PST 2009


Would it be worthwhile to use this jar for BioPortal?

Trish


>-----Original Message-----
>From: Timothy Redmond [mailto:tredmond at stanford.edu]
>Sent: Monday, February 02, 2009 4:27 PM
>To: Alan Ruttenberg
>Cc: Melanie Courtot; bioontology-support at mailman.stanford.edu; Trish
>Whetzel
>Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display
>
>
>> 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.
>
>Yes - your description is pretty much right on.  Protege is ignoring
>some of the owl:Ontology declarations which it should be using to
>determine the names of the imported ontologies.  After that imported
>data started to get lost.
>
>I have debugged this and Tania fixed it in the latest svn.  It is a pure
>and simple Protege bug and it made a mess of your imported assertions.
>I think that you can just drop and use the attached protege-owl.  For
>this style of ontology this is an important fix.
>
>-Timothy
>
>
>----- Original Message -----
>From: "Alan Ruttenberg" <alanruttenberg at gmail.com>
>To: "Trish Whetzel" <whetzel at stanford.edu>
>Cc: "Melanie Courtot" <mcourtot at gmail.com>, bioontology-
>support at mailman.stanford.edu, "Timothy Redmond" <tredmond at stanford.edu>
>Sent: Monday, February 2, 2009 3:15:34 PM GMT -08:00 US/Canada Pacific
>Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display
>
>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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