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[bioontology-support] Fwd: Problem with Bioportal display

Alan Ruttenberg alanruttenberg at gmail.com
Mon Feb 2 11:58:35 PST 2009


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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