Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [ncbo-execs] Fwd: [bioontology-info] bioportal

Nigam Shah nigam at
Fri Apr 23 20:18:41 PDT 2010

Dear Medha,

The error you are seeing is the result of an unfortunate situation of having
3 ways of accessing annotated resources (such as expression datasets)  at
Bioportal. Below I explain the three mechanisms and which work and which
don't. They are:

(1) via the 'All Resources' UI at (which
is in "alpha" status)

(2) via the Resources tab (e.g. at

(3) via the Resource index REST API (e.g. at

So, the content is there .. and (2) is just a nice way of seeing the same
information as in (3). In order to see the desired search result in the
resources tab (option 2, above), right now the steps are as follows:

- search for your desired term at:
- click on the term (column 1)  in the ontology of your choice .. e.g.
Melanoma in NCIT is the 12th one down.
- that will get you to:
- then click on the resource index (4 tabs to the left of the 'details').
- that shows you public datasets annotated with 'Melanoma'.

The UI at<>
the one that didn't work -- is being prototyped to avoid this circuitous
route of searching for annotated resources such as GEO datasets.
Unfortunately, when you tried it the alpha version (true to its status)
didn't work.

We will announce on the bioportal list when that UI is in production.
Meanwhile, the steps above will allow you to search bioportal for annotated

Best regards,

*From: *"Bhagwat, Medha (NIH/OD/ORS) [E]" <bhagwat at>
> *Date: *April 23, 2010 12:06:38 PM PDT
> *To: *"info at" <info at>
> *Cc: *"Bhagwat, Medha \(NIH/OD/ORS\) \[E\]" <bhagwat at>
> *Subject: **[bioontology-info] bioportal*
> Hi,
> I recently heard Mark Musen's talk and learnt that Bioportal can be used to
> search various resources such as expression datasets.  I tried using
> Today, I get request timed out message in the beginning even before typing
> any query.
> earlier, I had searched with term melanoma.  I don't get any results and
> but get the timed out message.
> Can you help?
> Medha
> _____________________________
> Medha Bhagwat, PhD
> Informationist
> NIH Library
> National Institutes of Health
> Building 10, Room 1L13F
> 10 Center Drive
> Bethesda, Maryland 20892-1150
> T. 301-496-2185
> F. 301-402-0254
> E. bhagwat at
> _____________________________
> Amazing Research. Amazing Help.
> _______________________________________________
> bioontology-info mailing list
> bioontology-info at
> _______________________________________________
> ncbo-execs mailing list
> ncbo-execs at
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list