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[bioontology-support] FW: Belated notes on bioportal

Natasha Noy noy at
Thu Apr 23 15:57:42 PDT 2009

I don't know if you want to reply to Sherri. But here is the info:
- the Search has been fixed (I think they tried it a while ago when  
there was a problem there)
- We will try to do something with breaking up the multiple values  
(say, having them on different lines). But we will probably not be  
able to strip some of the markup that is there in the values


On Apr 23, 2009, at 8:24 AM, Trish Whetzel wrote:

> 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 it.
> Tracy M. Safran
> Contractor - SAIC Frederick
> EVS support
> 301-402-1537
> 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 readable.
> Larry
> 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.)
> Sherri
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