[BioC] Creating annotation package with a new database schema

[Marc Carlson]

Hi Fabian,

Have you seen this function (it's in AnnotationForge)?

?makeOrgPackageFromNCBI


   Marc



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.
>
> kind regards, Fabian
>
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