[BiO BB] Advanced web query interfaces for biological databases

Mike Marchywka marchywka at hotmail.com
Wed Apr 9 12:58:08 EDT 2008

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
> http://www.bioinformatics.org/mailman/listinfo/bbb

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