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[bioontology-support] Fwd: Problem with Bioportal display

Trish Whetzel whetzel at stanford.edu
Sun Feb 1 18:29:19 PST 2009


Thanks, good to know.  BTW, do you know if there were any changes to the OBO
metadata file for OBI at:
http://www.berkeleybop.org/ontologies/obo-all/ontology_index.xml?

 

Trish

 

 

From: Melanie Courtot [mailto:mcourtot at gmail.com] 
Sent: Sunday, February 01, 2009 10:15 AM
To: Trish Whetzel
Cc: 'Alan Ruttenberg'; bioontology-support at mailman.stanford.edu
Subject: Re: [bioontology-support] Fwd: Problem with Bioportal display

 

 

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

 

Thanks,

Melanie

 

 

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





Comments in-line.

 

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?

 


In addition other cosmetic changes are still manifested on the page.
The order of the properties is poor. See
http://ashby.csail.mit.edu/cgi-bin/obiterm?ref=OBI_0000225

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 gmail.com>
Date: Fri, Jan 30, 2009 at 11:20 PM
Subject: annotation properties
To: Alan Ruttenberg <alanruttenberg at gmail.com>


They are duplicated in Bioportal too. e.g check material entity the in
branch annotation is repeated
http://bioportal.bioontology.org/visualize/39300/IAO_0000018
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

TFL- BCCRC

675 West 10th Avenue

Vancouver, BC

V5Z 1L3, Canada

 

 

 

 

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