[BioC] Editing AnnBuilder function "getSrcUrl"

[Nianhua Li]

Hi, Dermot,

I have updated AnnBuilder to support cattle. Please use "Bos taurus"
as organism name when you invoke ABPkgBuilder. Here is an example script:

library(AnnBuilder)
ABPkgBuilder(baseName="bovine.GenBankID",
                 baseMapType="gbNRef",
                 pkgName="bovine",
                 pkgPath=".",
                 organism="Bos taurus",
                 otherSrc="bovine.EntrezGeneID",
                 version="1.1.0",
                 author=list(
                   authors="myname",
                   maintainer="myname <user at email.com>"
                   )
                 )

"bovine.GenBankID" and "bovine.EntrezGeneID" are the mapping I
extracted from Affymetrix's annotation file for gene chip Bovine. I
also want to list the QC data here just to give a sense of annotation
coverage:

Mappings found for probe based rda files:
         bovineACCNUM found 24117 of 24128
         bovineCHRLOC found 9267 of 24128
         bovineCHR found 18687 of 24128
         bovineENTREZID found 19415 of 24128
         bovineENZYME found 1017 of 24128
         bovineGENENAME found 19045 of 24128
         bovineGO found 10914 of 24128
         bovineMAP found 245 of 24128
         bovinePATH found 2131 of 24128
         bovinePMID found 5747 of 24128
         bovineREFSEQ found 18740 of 24128
         bovineSUMFUNC found 0 of 24128
         bovineSYMBOL found 19045 of 24128
         bovineUNIGENE found 18952 of 24128
Mappings found for non-probe based rda files:
         bovineENZYME2PROBE found 358
         bovineGO2ALLPROBES found 5178
         bovineGO2PROBE found 3218
         bovineORGANISM found 1
         bovinePATH2PROBE found 165
         bovinePFAM found 14273
         bovinePMID2PROBE found 2929
         bovinePROSITE found 9818

In regarding to your question about Resourcerer, I am sure Jianhua,
the author of the Resourcerer package, will be the most helpful
resource. Speaking with my limited knowledge of Resourcerer, I think
no modification is required for function "getResourcerer" and you want
to specify organism name as "cattle". The function "resourcerer2BioC"
may not support cattle out of the box. One possible solution is to add
a mapping between "cattle" and "Bos taurus" inside the function code.
 But there must be other better solutions as well.

cheers

nianhua

Dermot Morris wrote:
> Hi Nianhua,
> 
> That would be a very useful development.  Does Resourcerer also have
> some
> Additional functions that need to be changed to accommodate "Bos Taurus"
> or is it dependent on calls to the same function as AnnBuilder? It's
> been a few weeks since I last looked.
> 
> There is no rush - any time in the next couple of weeks will be fine by
> me!
> 
> Dermot