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[bioontology-support] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at
Mon Feb 2 11:35:42 PST 2009

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






From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Trish
Sent: Saturday, January 31, 2009 9:56 AM
To: bioontology-support at
Subject: [bioontology-support] Fwd: Problem with Bioportal display
Begin forwarded message:

From: Alan Ruttenberg <alanruttenberg at>
Date: January 31, 2009 8:56:12 AM PST
To: Trish Whetzel <plwhetzel at>, Benjamin Dai
<benjamin.dai at>
Cc: Melanie Courtot <mcourtot at>
Subject: Problem with Bioportal display

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

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.


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


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