[BiO BB] ...biological databases/ another example- epitope prediction problem

Mike Marchywka marchywka at hotmail.com
Tue Apr 15 10:03:06 EDT 2008

I think I mentioned this much earlier but let me point to another situation I recently encountered.
There are several web sites with epitope prediction servers. The idea is you upload a peptide,
select a few parameters, and eventually you get back a list of possible epitopes along with some 
metrics. So, you may cut/paste a 1-10K sequence and get back hundreds of interesting things
and different servers may give different results. What do you expect a typical user to do with this data?

In my case, I had a more complicated task as I was looking for incorrectly translated base sequences
that could lead to accidental epitope matches with normal proteins. So, I had to use things
like fake ribosomes on some edited chromosome sequences, upload the hypothetical translation product to
a series of slicer and dicers ( epitope makers ) and then collate all the results, and then do blast
or other searches on these peptides. How do you do that with a web interface at every point?

Offhand, what is the use case for a web interface on an epitope server that will routinely
return 100's of hits with no uniform way to select interesting and uninteresting results?

Unfortunately, I had to write scripts to extract data from the html. In many cases, I could use lynx
to render the html so I didn't have to parse html source but you can't always rely on this. As html
is meant to be interactive, there is rarely a guarantee from the site that it will be stable. A simple
API with a text response option would have addressed my needs using results that the site
probably had to generate anyway to make the html results. Now, I don't expect ANSI to 
issue a standard for epitope information exchange, but there are formats ranging from simple 
text ( my preference ) to XML ( with lots of canned support) that can be easily parsed and remain
stable even as user artwork is changed to accomodate fashion fads.

You see this everywhere- from the Securities and Exchange Commission to the US patent office.
I hadn't realized that the API idea would need to be "sold" but I guess I under estimated how many people
think that the graphics are the model- and I think that I recognize the shortage of skilled people in the
computer area and the skill set that many professionals in the area possess so I guess I should have known
better :) So, if you are still not convinced and the moderator doesn't get annoyed, it may be worthwile
to continue this discussion and see if you have more objections that I can't satisfactorily address because
I consider it to be an important problem.

> From: marchywka at hotmail.com
> To: keithcallenberg at gmail.com; bbb at bioinformatics.org
> CC: golharam at umdnj.edu
> Subject: RE: [BiO BB] Advanced web query interfaces for biological databases
> Date: Tue, 15 Apr 2008 08:16:33 -0400
> 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

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