[Biophp-dev] Abstracting the parser backend

Serge Gregorio biophp-dev@bioinformatics.org
Wed, 30 Apr 2003 13:46:56 +0800


I'm now registered as user "flipmozart" at bioinformatics.org.
Kindly add me to the list of developers.  

Some quickie replies:

>B.t.w what a relief to write and read about stuff that matters!

HAHAHAHAHAHAHAHAhahaahahahahaahahaha!!!!  =)

On the Parser class issue, I haven't really waded deep into
the code.  However, by just reading the discussion so far,
it *SEEMS* the Parser class isn't far off from the IO class,
and may only differ in name and in scope/granularity.

May I suggest renaming it from "Parser class" to some other
name that is more "data-centric"?  I'll explain why later.

Btw, I have a question for Sean.  I've written an Amateur Gene 
Finder demo script at:


I'd like to make the protein sequences (e.g. GAVLIFYW) "clickable",
so that it forwards the string as a query to protein database sites like PROSITE, get info on it, an display this info in another PHP
page WITHOUT ever leaving the SF site.

My practical question is: can you eSearch/eUtils do this (or be
easily modified to do this)?  

Also, Sean's suggestion re: org structure is fine except that
GenePHP as originally conceived is not be limited to "genes".  
The term was coined to avoid conflicts with biophp.org.

However, I see nothing wrong with the project getting known as 
giving special emphasis on DNA and proteins, and being under the umbrella of a larger BioPHP project, hosted/administered here by

Lastly, to show that this is a team effort, I've revised the SF
site to make greater use of the word "PROPOSED" as in "Proposed GenePHP Bioinformatics Concept Map".  I do not want to convey
the impression that they are FINAL or CLOSED to discussion.  



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