Dear All

I generated a an OrgDb package for Salmo salar, using `AnnotationForge::makeOrgPackage()`. However, the sqlite table REFSEQ (containing RefSeq IDs) is missing when I load the package

libarary(org.Ssalar.eg.db)
columns(org.Ssalar.eg.db)
[1] "ACCESSION"    "CIGENE_ID"    "GENENAME"     "GENE_BIOTYPE" "GID"

But looking into the .db I can see the table is there

library(RSQLite)
con <- dbConnect(RSQLite::SQLite(), org.Ssalar.eg_dbfile())
> dbListTables(con)
[1] "cigene"       "gene_biotype" "gene_info"    "genes"        "map_counts"  
[6] "map_metadata" "metadata"     "refseq"   

It would be nice if someone could explain why the REFSEQ table is not accessed from AnnotationDbi, i guess it's realted to AnootationDbi filtering the table out... But I would like to get this package at some point onto BioConductor and thus it would be nice to keep the table called REFSEQ.

cheers, F

I'm not sure you will ever need to get this package into Bioconductor, as there are already two such packages available via AnnotationHub.

> library(AnnotationHub)

> hub <- AnnotationHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2016-10-11
> query(hub, "Salmo salar")
AnnotationHub with 2 records
# snapshotDate(): 2016-10-11
# $dataprovider: NCBI, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Salmo salar
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH13851"]]'

            title                    
  AH13851 | org.Salmo_salar.eg.sqlite
  AH48629 | org.Salmo_salar.eg.sqlite

Also do note that the ACCESSIONS column should be doing a query on your refseq table. You are confusing the available columns that you can use with select or mapIds and the underlying SQL tables that will be queried. But all of the underlying SQL is generated based on the DB schema, so I can't say for sure, since you don't say exactly how you generated that package.