[BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package

[Marc Carlson]

Hi Sashi,

The PDF from Gabor that you are looking at is much older and was from 
before we even had the select method.  These days you probably don't 
want to do that.  Especially if you want to implement a method like 
select().  I strongly suspect that you really just want to be looking at 
this vignette instead:

http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewAnnotationPackages.pdf

To answer your questions, GO is actually looking at a view that is 
created in the database of the three GO tables (one for BP, MF and CC).  
But you probably don't need that level of detail.  If you are using 
org.At.tair.db to look at arabidopsis, then you may already have 
everything you need.  And if you need another organism, you probably 
want to look 1st at making an org package using 
makeOrgPackageFromNCBI().  And if for some reason you want to expose 
some entirely new database resource (IOW you don't want to make an 
organism package but something else entirely), then you might need to 
use the vignette above.

I hope this helps you,


   Marc



On 08/13/2013 04:33 AM, Rameswara Sashi Kiran Challa wrote:
> 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]]
>
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