[BiO BB] Advanced web query interfaces for biological databases
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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> > BBB at bioinformatics.org
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