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] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Mon Feb 2 12:01:30 PST 2009


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?
>>
>>




More information about the bioontology-support mailing list