[BiO BB] Advanced web query interfaces for biological databases

Keith Callenberg keithcallenberg at gmail.com
Sun Apr 13 20:23:30 EDT 2008

Thanks for your suggestion, Mike. As a developer I also value the
concept of an open and freely available API, and I wish that more
sites would provide these, but I am not sure it is yet appropriate for
our database as it will be some time before we have a sizable pool of
users, letalone developers.

Also, I might not be clear on what you mean by "programmatically," but
I think it is a bit short-sighted to limit the scope of web-based
interfaces to only casual queries. I am not usually a supporter of the
term "Web 2.0" because I think it has lately signified little more
than colorful buttons, but I do believe more and more tasks can be
accomplished from within the browser. I believe energy should be put
into moving more advanced tasks online because it removes learning
curves and hardware restrictions, thereby increasing your base of

I think it is not easy to develop an intuitive web-based UI that is
not fairly restrictive, but that does not mean it should not be


On Wed, Apr 9, 2008 at 9:58 AM, Mike Marchywka <marchywka at hotmail.com> wrote:
>  As I  suggest to anyone who will listen, provide an API ( a machine usable interface) to let
>  third parties ( as well as yourself ) design whatever UI's you determine make sense.
>  Any complicated data source is best accessed programmatically and a web interface is only
>  useful for the casual user doing one-of situations or exploratory work. In some cases,
>  this may be the full extent of the immediate need. Unless you think are can anticipate
>  every need that every user may have with your data source, an API that exposes all
>  the data that you are willing to reveal is the best way to go.
>  So, I'd recommend publishing an API and even sample scripts for your own developers
>  first and then worry about some specialized web interfaces.
>  Mike Marchywka
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>  > Date: Wed, 9 Apr 2008 00:07:47 -0700
>  > From: kcallenb at email.sjsu.edu
>  > To: bbb at bioinformatics.org
>  > Subject: [BiO BB] Advanced web query interfaces for biological databases
>  >
> > I am working on the web interface for a fairly complex database that
>  > integrates several different types of data (gene expression, sequence,
>  > annotation). A basic interface for accessing individual records in the
>  > database has already been written, but my lab's biologists would like
>  > to see a more powerful form interface. They would like to be able to
>  > add thresholds on arbitrary fields and set other parameters for
>  > several fields at a time.
>  >
>  > I have been pointed to the Query Builder on NCBI's Trace Archive
>  > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept,
>  > and I can see how that could be implemented with its helpful
>  > auto-complete text, but it seems like it still has quite a learning
>  > curve and is not really very intuitive. I have also found BioCyc.org's
>  > Advanced Query page (http://biocyc.org/query.html) and several others
>  > that are similar or harder to use. AJAX can help, and we plan to
>  > integrate auto-completion of some text, but I would like to build
>  > something powerful and yet intuitive that does not require someone to
>  > read a manual before using. Any suggestions? I suppose innovation in
>  > UI design often starts in other places first so I'd appreciate any
>  > non-biological examples as well.
>  >
>  > Thanks!
>  >
>  > Keith Callenberg
>  >
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