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

[Sashi]

Marc Carlson <mcarlson at ...> writes:

> 
> 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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Hi Marc,

Thanks for your prompt reply. Referring to the document you pointed me to, I
created another R script within the organism package skeleton( an R script
apart from zzz.R) and set cols, keytypes accessor methods. 

As part of annotation packages Bimaps are created in every annotation
package. How do we use these Bimaps in these accessor methods? Am I right in
thinking that these Bimaps are to be used in these accessor methods? Or
those Bimaps have to be accessed only via get(), mget(), toTable() methods? 

Also, can you please let me know if there is any documentation available on
how the GO views are created? I see there are seperate tables like go_cc,
go_mf, go_bp, etc under Arabidopsis annotation package. Is it necessary to
have go_cc, go_mf, go_bp, go_mf_all, like tables in the sqlite database for
the customized annotation package I am creating? Will not just a single
table for all GO annotations suffice?

Thanks again for your time,
Sashi
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