[BioC] annotation package for ecoli2

[Nianhua Li]

Hi, Caroline and Yanqin,

It is not easy to generate annotation packages for E. coli by using AnnBuilder,
more specifically the ABPkgBuilder function. The set of source databases we used
don't provide annotations for GO, UniGene, genome map location, PROSITE and PFAM
for E. coli. For the rest of the annotations: gene name, symbol, PubMed and
Refseq mappings are from Entrez Gene, pathway and enzyme information are from
KEGG. All annotations are based on Entrez Gene ID. 

If there is a better Gene Identifier in the E. coli community (other than Entrez
Gene ID) or if you have a better source than Entrez Gene or KEGG, it will make
more sense to create a seperate builder for E. coli annotations than to
manipulate ABPkgBuilder.

If you think Entrez Gene and KEGG are good sources for E. coli annotation, then
we can try to "hack" ABPkgBuilder. If you could provide the sources for the
missing annotations, I can help you to "hack" ABPkgBuilder or maybe build the
package for you. 

thanks

nianhua

Nianhua Li
Computational Biology, PHS, FHCRC