Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Nick Griffith ngriff at stanford.edu
Thu Feb 5 11:22:58 PST 2009


any chance other people would download this jar first to be guinea  
pigs and make sure there's no quirks with it?


On Feb 5, 2009, at 11:11 AM, Natasha Noy wrote:

> I think it would make sense to replace the protege-owl.jar with this
> one.
>
> Natasha
>
>
> On Feb 2, 2009, at 6:19 PM, Trish Whetzel wrote:
>
>> 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?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>>>
>> <protege-owl.jar>_______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




More information about the bioontology-support mailing list