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[bioontology-support] FW: Belated notes on bioportal
whetzel at stanford.edu
Thu Apr 23 08:24:26 PDT 2009
FYI - comments on new version of BioPortal.
From: Sherri De Coronado [mailto:decorons at mail.nih.gov]
Sent: Wednesday, April 22, 2009 9:41 AM
To: Trish Whetzel
Subject: Belated notes on bioportal
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.
NOTES FROM FOLKS AT NCI:
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
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 http://stage.bioontology.org/visualize/39478/Glioblastoma
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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