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[bioontology-support] Fwd: Problem with Bioportal display

Melanie Courtot mcourtot at
Sun Feb 1 10:15:12 PST 2009

I sent an email to Tim on Friday morning reporting the rendering  
problem with annotation properties in Protege 3.


On 1-Feb-09, at 3:15 AM, Trish Whetzel wrote:

> Comments in-line.
> From: bioontology-support-bounces at [mailto:bioontology-support-bounces at 
> ] On Behalf Of Trish Whetzel
> 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 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?
> In addition other cosmetic changes are still manifested on the page.
> The order of the properties is poor. See
> First subclass of, then definitions, then other annotation properties.
> The "Rdf Type" style of spelling of properties is unsightly. Known OWL
> and RDF defined properties should be displayed with better labels.
> This has been reported as a Feature request.
> There is way too much wasted space.
> A new UI is currently being developed and better page layout is part  
> of the design.
> There ought to be a search box for other OBI terms on the page,
> ideally with ajax auto completion. Be sure, if you do this, to include
> both leading string matches and internal string matches, in that
> order.
> Agreed and has been added as a Feature Request.
> To note, I have been receiving complaints about the display of OBI in
> Bioportal. I'd appreciate your prompt attention to detail here. What
> may seem to be minor issues from an engineering point of view,
> cumulatively reflect poorly on OBI and the BioPortal.
> Regards,
> Alan
> ---------- Forwarded message ----------
> From: Melanie Courtot <mcourtot at>
> Date: Fri, Jan 30, 2009 at 11:20 PM
> Subject: annotation properties
> To: Alan Ruttenberg <alanruttenberg at>
> They are duplicated in Bioportal too. e.g check material entity the in
> branch annotation is repeated
> Would you mind having a look at the released file? in branch appears
> only once, extra ones probably come from iao import?
> Seems to be proper inferred hierarchy, device is under artifact  
> object.
> Their server is very slow right now, so that's it for now.
> Worried about annotation properties :(
> Melanie

Mélanie Courtot
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

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