[BioC] org.Dm.egACCNUM2EG

[Tiandao Li]

Dear Marc,

Thanks for your response. I blasted my sequences against nr, nt, swissprot 
databases. Since no protein IDs are supported in these annotation 
packages, however I still can't get EG ids from nt BLAST search. I am 
thinking do blast search against Unigene Drosophila (Nucleotide) or any 
other databases, is it OK?

I tried to install biomaRt on my Ubuntu box for a week, and it always came 
the same wrong msg. I just don't know how to handle it.

Thanks,

Tiandao

> source("http://bioconductor.org/getBioC.R")
> getBioC("biomaRt",lib="/usr/local/lib/R/site-library/")
Running biocinstall version 2.1.8 with R version 2.6.0 
Your version of R requires version 2.1 of Bioconductor.
also installing the dependencies $B!F(JRCurl$B!G(J, $B!F(JXML$B!G(J

trying URL 
'http://bioconductor.org/packages/2.1/extra/src/contrib/RCurl_0.8-3.tar.gz'
Content type 'application/x-gzip' length 218153 bytes (213 Kb)
opened URL
==================================================
downloaded 213 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.93-2.tar.gz'
Content type 'application/x-gzip' length 870234 bytes (849 Kb)
opened URL
==================================================
downloaded 849 Kb

trying URL 
'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.1.tar.gz'
Content type 'application/x-gzip' length 275514 bytes (269 Kb)
opened URL
==================================================
downloaded 269 Kb

* Installing *source* package 'RCurl' ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package 'RCurl'
** Removing '/usr/local/lib/R/site-library/RCurl'
* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package 'XML'
** Removing '/usr/local/lib/R/site-library/XML'
* Installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: RCurl
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, 
lib.loc = lib.loc) :
  there is no package called 'RCurl'
Error: package 'RCurl' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'biomaRt'
** Removing '/usr/local/lib/R/site-library/biomaRt'

The downloaded packages are in
        /tmp/Rtmp3SQVK7/downloaded_packages
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'RCurl' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'XML' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'biomaRt' had non-zero exit status
> sessionInfo()
R version 2.6.0 (2007-10-03) 
i486-pc-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.0 



On Fri, 2 Nov 2007, Marc Carlson wrote:

Tiandao Li wrote:
> Hello,
>
> Recently I installed org.Dm.eg.db for GO analysis. My sequences were 
> blasted against siwssprot, using the following format in the annotation 
> part of genepix files
>
> ID	Name
> 16A-A02.g	P80096
> 16A-A03.g	Q9U572
> ...
>
> I tried org.Dm.egACCUM2EG$"P80096" to get Entrez gene id. and it came with 
> NULL. How can I get EG from swissprot acc?
>
I am afraid that the answer is that the ACCNUM maps are for genbank IDs
only.  Because of the way that NCBI handles genebank and its affiliated
nucleotide sequences, genebank accessions are sometimes connected to
TrEMBL (translated sequences), but never to Swissprot IDs.  Swissprot
IDs have not been included in our annotation packages before.  In the
past, the focus of the annotation packages has been to make them
gene-centric and so to date no protein-centric IDs have been included in
these packages.

However, the data packages are a work in progress and we are always
interested in user feedback to make them better.  Do you feel that there
is a wide reaching need for the associated protein IDs to be mapped in
to these annotation packages?  If you feel this is so, please let us
know what you think. 

In the meantime I believe that the biomart package can be used for
mapping your swissprot IDs.

    Marc