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[bioontology-support] FW: Belated notes on bioportal

Trish Whetzel whetzel at
Thu Apr 23 08:24:26 PDT 2009

FYI - comments on new version of BioPortal.


From: Sherri De Coronado [mailto:decorons at] 
Sent: Wednesday, April 22, 2009 9:41 AM
To: Trish Whetzel
Subject: Belated notes on bioportal


Hi Trish,
I think that I may never have forwarded these to you.  I was waiting for
additional comments, and forgot to send these when I didn't get any others.
So, in case I didn't forward, here are comments from two EVS staff.

Thanks, Sherri


I really like the categorized ontologies.  If I only care about anatomy, I
only search the ontologies in the Anatomy category.  The wait screens give
feedback that it is loading, rather than just sitting there.
The welcome screen is a little intimidating, but not that hard once you read

Tracy M. Safran
Contractor - SAIC Frederick
EVS support

Some things are improved and might be useful, but others (including some
essentials) are still seriously broken.  Two examples:
1.     Select NCIt and "Jump to" Glioblastoma, and you get Mouse
Glioblastoma - no hint that you've missed the main (human) Glioblastoma
concept (actually, doing it a 4th time now, I get a search pop-up that hints
at all the other candidates, but selecting a likely one does nothing).  The
only way I could get there was to slowly crawl the hierarchy.

2.     Full_Syn, Alt_Definition, and other subfield contents are
concatenated unreadably, then strung in a long comma-delimited list (having
got there, look at

While interesting as an experimental environment for ontologies, it still
doesn't seem geared to providing user-friendly access to content.  Which is
sad, because there is lots of good stuff there.

One simple-minded rule for properties with sub-fields would be, instead of
concatenating, show each sub-field separated by " | ", and for repeating
properties to start each property occurrence on a new line.  I'm sure they
could do better, e.g. using tables, but this would at least make them

Love it -- this is really cool.  Lots of neat new features that overall are
a  great improvement.  Really like the new look and feel.  As Larry says
above, still some problems with searching, at least in NCI Thesaurus.  For
example, I type "apoptosis" in jump to box, and wait for the list to come
up, select apoptosis, hit "go", and it still goes to "apoptosis pathway".
Perhaps I am doing something wrong, but if so, it's not intuitively obvious
how to make it go to the desired term.  I think it may actually not be using
Preferred_Name to retrieve the class. (I already submitted two other small
bugs to Natasha.)


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