[BioC] AnnBuilder and Diverse Mappings

[John Zhang]

>
>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 ...

I would map everything to Entrez Gene id and then use the mapping as the base 
file for ABPkgBuilder to build the annotation.



>
>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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>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084