[BioC] org.Hs.eg question

[Rhoda Kinsella]

Hi Sim and Marc,
You should forward this query to helpdesk at ensembl.org and someone will  
be able to help.
Regards,
Rhoda


On 19 Mar 2009, at 19:15, Marc Carlson wrote:

> Hi Sim,
>
> I can explain this, and maybe you can even help me to improve things.
> The mappings for ensembl protein and transcript IDs are available  
> mapped
> to ensembl gene IDs from ensembls web site (as mapped to ensembl gene
> IDs).  And the mappings from entrez gene to ensembl gene IDs presently
> come from NCBI.
>
> However, the gene to gene mappings from NCBI do not seem to be as
> complete as whatever ensembl is using, and I do not have any  
> explanation
> from them about why that is.  I also don't have a better source for  
> this
> information (yet) as I have been unable to locate this kind of
> information from ensembls FTP sites.  Something must exist somewhere  
> at
> ensembl though because the ensembl web site is presumably based on it.
> But whatever they are using at ensembl they do not seem to be sharing
> that mapping with the world (although it would be great to find out  
> that
> I had just missed it somehow).  If you know where I can find a better
> source for this kind of information than what I am currently using, I
> would be more than happy to consider it.  But it obviously has to be
> from a trustworthy and documentable source (such as NCBI or ensembl).
> Otherwise there would not be much point in including it.  ;)
>
>
>  Marc
>
>
>
>
> Sim, Fraser wrote:
>> Hi,
>>
>> I'm using the org.Hs.eg annotation package to convert Ensembl protein
>> annotations to Entrez GeneIds. I don't understand why although I can
>> find the correct annotation manually via the Ensembl website (EG =
>> 4340), the annotation package is unable to.
>>
>> Here is the code:
>>
>>> HsENSP
>>>
>> [1] "ENSP00000373017"
>>
>>> require("org.Hs.eg.db")
>>> HsEG = as.character(unlist(mget(HsENSP, org.Hs.egENSEMBLPROT2EG,
>>>
>> ifnotfound = NA)))
>>
>>> HsEG
>>>
>> [1] NA
>>
>> Thanks for any input.
>>
>> Regards,
>> Fraser
>>
>>
>>
>>> sessionInfo()
>>>
>> R version 2.8.1 (2008-12-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets   
>> methods
>>
>> [8] base
>>
>> other attached packages:
>> [1] gplots_2.6.0        gdata_2.4.2         gtools_2.5.0
>> [4] bioDist_1.14.0      RColorBrewer_1.0-2  GEOquery_2.6.0
>> [7] RCurl_0.94-0        rae230a.db_2.2.5    org.Rn.eg.db_2.2.6
>> [10] hom.Rn.inp.db_2.2.5 org.Hs.eg.db_2.2.6  RSQLite_0.7-1
>> [13] DBI_0.2-4           AnnotationDbi_1.4.2 Biobase_2.2.1
>> [16] rcom_2.0-4          rscproxy_1.0-12
>>
>>
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>>
>>
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.