[BiO BB] Advanced web query interfaces for biological databases

[Ryan Golhar]

I support this view.  "Programmatically" means allowing outside users 
developing their own software interfacing with your database/website via 
an API.

Although NCBI has a fairly well developed website, there is a lot I 
can't do from a GUI because of the amount of data we work with.  It 
easier for us to use NCBI's API (E-utilities) to access their live 
database and extract information in a way we need.

Anyone who works with lots of data will know a GUI interface will never 
be sufficient.  Its much easier to accomplish the work with a script or 
program.


Mike Marchywka wrote:
>> our database as it will be some time before we have a sizable pool of
>> users, letalone developers.
> 
> And what kind of interface will your few developers use? I guess my point is that if you have
> a compelling data set, developers will come out of the wood work to support it.
> 
>> 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'm not advocating intentional limitations, just expressing the problem with a GUI. You
> end up guessing how a user wants to work ( or you are omniscient). For examples
> or introductory material that is great and even important for proof of concept if
> nothing else. To let motivated users exploit the full capabilities of most data sources,
> however, you need to let them ( or their machines ) interact with existing tools.
> 
> Further, if you define a machine usable interface (API) you better document your features
> without having to worry about modal dialogs and button colors.
> 
> 
> 
> Mike Marchywka
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> 
>> Date: Sun, 13 Apr 2008 17:23:30 -0700
>> From: keithcallenberg at gmail.com
>> To: bbb at bioinformatics.org
>> Subject: Re: [BiO BB] Advanced web query interfaces for biological databases
>>
>> 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
>> users.
>>
>> 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
>> pursued.
>>
>> Keith
>>
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