[BioC] Creating annotation package with a new database schema

[Fabian Grammes]

Hi Hervé

Thanks a lot, that was exactly the information that I've been
looking for !

After updating BioConductor today, I am struggling a bit with
getting the code to work again, but that should be fixed tomorrow
I hope :)

@ Marc

I've checked the function: makeOrgPackageFromNCBI,
however since I have most of my annotation information stored locally
(GO etc. - obtained via Blast2GO) and not yet available at NCBI,
I do not think the function helps in my case.

cheers, F

On Oct 23, 2012, at 12:04 AM, Hervé Pagès wrote:

> Hi Fabian,
>
> On 10/22/2012 05:57 AM, Fabian Grammes wrote:
>> Dear List
>>
>> I am working with Atlantic salmon and am highly interested to make a
>> custom annotation package for the
>> microarray that I am using.
>>
>> I've worked through the tutorial from Gabor Csardi ("Creating an
>> annotation package with a new database
>> schema" ), which was very helpful. However, I am struggling to  
>> implement
>> the bimap objects to access
>> the GO annotations that I have in the DB.
>>
>> The GO data is stored in 6 tables (BP, BP_all, MF, MF_all, CC,  
>> CC_all)
>> looking like the format that I found for
>> the organism packages in BioC:
>> ID        GOID            evi
>> 6092    GO:0000910        IEA
>> 6092    GO:0040035        IEA
>> 6092    GO:0000398        IEA
>>
>> So if someone could help me/ point me to the correct way how to
>> implement the GO mappings
>> in an annotation package that would be great.
>
> If you look for example at the hgu95av2.db package, it provides 3
> predefined Bimaps for accessing the GO data: hgu95av2GO (GO map),
> hgu95av2GO2PROBE (GO2PROBE map), and hgu95av2GO2ALLPROBES  
> (GO2ALLPROBES
> map). The 1st is a direct map, the 2nd and 3rd are reverse maps:
>
>  > direction(hgu95av2GO)
>  [1] 1
>  > direction(hgu95av2GO2PROBE)
>  [1] -1
>  > direction(hgu95av2GO2ALLPROBES)
>  [1] -1
>
> All of them are of class "ProbeGo3AnnDbBimap".
>
> The predefined Bimaps are created at load-time. The direct maps
> with a call to AnnotationDbi:::createAnnDbBimaps() and the reverse
> maps by "manually" reversing some of the direct maps returned by
> createAnnDbBimaps().
>
> So you need to add an entry for the GO map to the list of "seeds"
> passed to createAnnDbBimaps(). In your case this entry needs to look
> something like (assuming ID is your internal id for genes):
>
>  seeds <- list(
>    ...
>    list(
>        objName="GO",
>        Class="ProbeGo3AnnDbBimap",
>        L2Rchain=list(
>            list(
>                tablename="probes",
>                Lcolname="probe_id",
>                Rcolname="gene_id",
>                filter="{is_multiple}='0'"
>            ),
>            list(
>                tablename="genes",
>                Lcolname="gene_id",
>                Rcolname="ID"
>            ),
>            list(
>                Lcolname="ID",
>                tagname=c(Evidence="{evi}"),
>                Rcolname="GOID",
>                Rattribnames=c(Ontology="NULL")
>            )
>        ),
>        rightTables=c(BP="BP", CC="CC", MF="MF")
>    )
>    ...
>  )
>
> Then:
>
>  ann_objs <- createAnnDbBimaps(seeds, seed0)
>
> where 'seed0' is defined by something like:
>
>  seed0 <- list(objTarget="chip <name_of_your_chip>",
>                datacache=datacache)
>
> and 'datacache' is the environment that will be used for package-level
> caching of the data loaded from the DB (use NULL for no caching, I'm
> assuming those extra details, which are not GO-specific, are covered
> in Gabor's document, but I don't know).
>
> Then you can append the reverse maps to 'ann_objs' with something  
> like:
>
>  ## Append GO2PROBE map:
>  map <- ann_objs$GO
>  map <- revmap(map)
>  map at objName <- "GO2PROBE"
>  ann_objs$GO2PROBE <- map
>
>  ## Append GO2ALLPROBES map:
>  map <- ann_objs$GO2PROBE
>  map at rightTables <- c(BP="BP_all", CC="CC_all", MF="MF_all")
>  map at objName <- "GO2ALLPROBES"
>  ann_objs$GO2ALLPROBES <- map
>
> All this needs to happen at load-time (via the .onLoad hook). Again  
> I'm
> focusing on the GO-specific part of the story here, assuming that  
> you've
> already managed to create the non-GO specific maps (thanks to Gabor's
> document).
>
> Hope this helps,
>
> H.
>
>>
>> kind regards, Fabian
>>
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>
> -- 
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
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