[BiO BB] ontology/controlled vocabulary for SNP "molecular phenotype", effects on coding

[Ann Loraine]

Hi,

I have two questions for the list:

First question:

I'm looking for a classification system (ontology, controlled
vocabulary) to describe the location and effects of various SNP
alleles on protein and gene sequence.

For example, this system would have controlled vocabulary terms to
describe when a SNP is located in a translated region and changes (or
doesn't change) the amino acid sequence of a protein.

Ultimately, I'd like to be able to treat these controlled vocubulary
terms as categorical variables in a QTL analysis, for example.

Does such a thing exist?

Second question:

I'm looking for a system that can classify SNP alleles given their
genomic location and their "base" relative to a reference genomic
sequence. For example, I would tell the system that my SNP allele is
base 'A' at posiition 100,345 on chromosome 1, and then it would tell
me how the allele affects known gene(s) in that region, ideally using
the controlled vocabulary from Question 1.

Any tips, pointers, rumors, advice would be much appreciated!

-Ann

-- 
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org