[BioC] AnnBuilder and Diverse Mappings

[Johannes Graumann]

So here's the entire dilemma:

Total Entires:  52735   Unique Protein Index

AnnBuilder usable(?; I didn't find a suitable baseMapTyype for Entrez
despite the post mentioning it) mappings:
        47787   Entrez Gene Number
        24414   GenBank
        32158   RefSeq
        39079   unigene

Further there are Swiss-Prot, TrEMBL, Ensembl, UNIPARC and Vega mapping -
all for a subset ...

How would you do it?

Joh

Johannes Graumann wrote:

> Hello,
> 
> I'm trying to build an annotation package for one of EBIs IPI data base
> using AnnBuilder. I'm trying to pull in the GO annotation unsing the mixed
> GenBank/RefSeq baseMapType, but the database is build from a very diverse
> set of sources and a significant number of entries has neither GenBank nor
> RefSeq IDs. The question to more advanced users is now: how would you
> proceed in this case? Is there a way to pull in Info using different
> baseMapTypes and than unify the outputs?
> 
> Please advise,
> 
> Joh
> 
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