Hi ,

I am trying to build an annotation organism package by using Annotation
Forge package. I followed this
document<http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/NewSchema.pdf>written
by Gabor Csardi.
I was able to build a sqlite database and create an Annotation package
using the makeAnnDbPkg() function.

I understand cols(), keys(), keytypes() and select() are set as generic
methods in AnnotationDbi.

When I look into methods-AnnotationDb.R script in AnnotationDbi package, I
see cols() method is set and it actually reads all the columns of all the
tables in the sqlite table.

When I run *cols() *on *org.At.tair.db  *I get few values which are
actually not field/column names in the sqlite db. For Eg. there is no table
called "GO" in org.At.tair.sqlite database. I am unable to understand how
it creates these values. Could someone please help me understand how and
where exactly these accessor functions are defined and how and where are
they to be modified to be able to access the data in the sqlite db that I
am creating for the organism I am working on.

==========================

> cols(org.At.tair.db)

 [1] "TAIR"         "CHRLOC"       "CHRLOCEND"    "ENZYME"       "PATH"


[6] "PMID"         "REFSEQ"       "SYMBOL"       "GENENAME"     "GO"


[11] "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL"

[16] "ARACYC"       "ARACYCENZYME" "ENTREZID"     "CHR"
=======================================

Please point me to any documentation available for the same.

Thanks for your time,
Sashi

	[[alternative HTML version deleted]]

