[BiO BB] Advanced web query interfaces for biological databases

Mike Marchywka marchywka at hotmail.com
Tue Apr 15 08:16:33 EDT 2008


The punchline, repeated below, is that you still need someway to get 
your GUI to talk to your data source.
I guess we are just arguing over publication and stability of the interface.

> Date: Mon, 14 Apr 2008 21:49:54 -0700
> From: keithcallenberg at gmail.com

>
> I completely agree that there are significant limitations to user
> interfaces, but there is a reason why at least half of NCBI's users
> use their web-based tools when they are applicable, and it is that

I routinely use pubmed myself, for the reasons stated ( exploratory 
browsing ) and I am not claiming this is irrelevant. But, they could have implemented
it as a simple web form that called their eutils API and achieved both 
results with little duplicated effort. 

> doing so is often simpler and saves time from installing BLAST, ORF
> Finder, etc on your machine, having to download the data, and making
> sure you are using the correct command-line options.

Most of this is unrelated as I generally don't download databases ( to save
disk space and use the current data and offload look up to a real server).
I'm thinking about things like http GET or POST requests that are 
documented and stable ( but you could think about binary socket protocols if
you really want to get extreme) . If you publish these as your site develops, 
anyone with an immediate need for your data can access it while you still
pick colors for your buttons and escape routes from modal dialog boxes.
Many local installs still communicate through ports and may or may not
use http over their sockets.

There is also a trivial but annoying limitation with some GUI-only sites
that you can't post a link ( in a forum like this) to a particular result
and you need to write a paragraph explaining how to find some simple
thing like a particular article or molecule. 
A simple API based on http GET requests normally lends itself to tractable link creation. 


>
> I guess my point of disagreement with Mike is the order or priority in
> development, because I do not claim that having an API and/or publicly
> available database is not important. It is just that it would not make
> sense, at least for our project, to focus on a minority of power users
> without first accommodating the base of users who are biologists not
> bioinformaticians.

I don't offhand think that biologists are computer illiterate and in
any case am not advocating making things unfamiliar to your intended audience.
However, even for the computer illiterate, it would probably be a more useful
learning curve to learn SQL syntax than navigation of a data-specific GUI
unless the latter is incredibly intuitive. And, in the absence of that, I would think 
that the motivated biologist could find someone who knows SQL. So, I'm just
suggesting that a parameterized version of a well known interface like
SQL ( with a list of parameters specific to your data ) would not just address
power users and may even be more beneficial for your users. 

And, you still need someway to get your GUI to talk to your data source.
I guess we are just arguing over publication and stability of the interface.



>
> Keith
>
> On Mon, Apr 14, 2008 at 8:19 PM, Ryan Golhar  wrote:
>> 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
>>> 586 Saint James Walk
>>> Marietta GA 30067-7165
>>> 404-788-1216 (C)<- leave message
>>> 989-348-4796 (P)<- emergency only
>>> marchywka at hotmail.com
>>> Note: If I am asking for free stuff, I normally use for hobby/non-profit
>>> information but may use in investment forums, public and private.
>>> Please indicate any concerns if applicable.
>>> Note: Hotmail is possibly blocking my mom's entire
>>> ISP - try me on marchywka at yahoo.com if no reply
>>> here. Thanks.
>>>
>>>
>>>
>>>> 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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>>
>>

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