[Bioperl-l] Entrez Gene ASN

Stefan Kirov skirov at utk.edu
Thu Mar 10 09:14:40 EST 2005

Hi guys!
I have done some (mostly) serious thinking about ASN Entrez Gene parsing 
and I propose we do my favorite thing- postpone everything we cannot 
deal with right now. If you want it to sound better: take a gradual 
approach where we store the data we can deal with in the existing 
Bioperl objects and skipping the rest for now.
In details:
ASN gene record can be correctly represented as a tree. I have written a 
simple parser for my own purposes which is storing the following:
What I do then is get specific levels and tags and build different 
objects. So level 2 with parent EntrezGene (which is the root level and 
has no information) is gene description and has tags such as gene, name, 
etc; at level 3, 5 and 6 you can get the complete specie definition by 
looking for orgname and org as tags and records with parent mod (which 
is a value for orgname, descend down the branch).
I am using this approach to store most of the data in a relational 
database without going through Bioperl. What I ultimately want to do is 
use standard Bioperl modules. However, I don't think we have an object 
that can efficiently represent the structure (correct me if I am wrong). 
I think it may be a good idea to have a container object, possibly 
Bio::Gene that may contain multiple Bio::Seq objects (with or without 
real sequence). I believe we can borrow some structure and code from 
EnsEMBL gene representation (way to contain multiple transcripts, etc., 
not the database interactions certainly).
Please let me know what you think.

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