[BioC] Re: Annotate clones Bioconductor beginner

John Zhang jzhang at jimmy.harvard.edu
Mon Dec 1 16:33:53 MET 2003

>From: "Law, Annie" <Annie.Law at nrc-cnrc.gc.ca>
>To: "'jzhang at jimmy.harvard.edu'" <jzhang at jimmy.harvard.edu>
>Cc: "'bioconductor at stat.math.ethz.ch'" <bioconductor at stat.math.ethz.ch>
>Subject: Annotate clones Bioconductor beginner
>Date: Mon, 1 Dec 2003 09:18:14 -0500 
>MIME-Version: 1.0
>Hi John,
>I am new to BioConductor and would appreciate advice with the following.
>My goal is to take cloneID's from for example Human microarray 19K human
>and find out the corresponding accession number and subsequently Unigene
>I would like to keep a database of this information.

You can download the "Annotation CSV" (or other format) for your chip from  
"http://www.affymetrix.com/analysis/download_center.affx". The file contains 
mappings to GenBank accession numbers, Unigene ids, and other information.

>I would also like to know if a cloneID has changed and if so note this
>is the database and also update any corresponding information.
>I would like to know what the best way is to proceed with this.
>I have looked at the vignettes and it seems that the AnnBuilder
>package should be used instead of the annotate package?

AnnBuilder is for building annotation data packages. It does not have the 
function of keeping track of the history of cloneIDs.

>I went to the I.M.A.G.E. consortium and found out that they have an ftp 
>site where I can download a file including information for all clones
>IMAGE cloneID and Genbank accession numbers among other fields.
>My first goal in this project would be able to compare my list of cloneIDs
>the file available on the I.M.A.G.E. consortium ftp site.
>However, I don't think that I can use the ABPkgBuilder since it requires a
>text file with two columns and the I.M.A.G.E. consortium site is not one of
>accepted sites for the ABPkgBuilder.
>Any suggestions?

AnnBuilder does not have built in parsers to parse data from I.M.A.G.E. However, 
you may write your own parser to parse the data from I.M.A.G.E or other sources 
using AnnBuilder. Have a look at the parsers in the "data" directory for the 
release verion or "scripts" directory for the developmental version of 
AnnBuilder for exmaples of parsers. 

>If somehow I do get the list of my cloneIDs and corresponding accession
>I think I will be able to use the ABPkgBuilder.  Is this true?

Yes, you can use AnnBuilder to build an annotation data package like those 
available from the Bioconductor web site.

>Also where can I look for information on dumping results form AnnBuilder
>into a database?

AnnBuilder also generates XML files containing annotation data. You may try to 
parse the XML files and dump the data into a database. 

>Are there tracking tools within BioConductor, AnnBuilder?
>For example, is there a tracking tool available to let you know if a cloneID
>has changed?

No, AnnBuilder does not do that.

>what is the best way to create a user friendly interface with BioConductor?
>Is there a GUI interface tool available in the BioConductor package?
>If not I may think of creating my own web interface or dumping the
>information from the data base on an Excel sheet.

R has a tcltk package for building GUI interfaces. 
http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/ has examples of 
constructing common widgets using R. Bioconductor's widgetTools and tkWidgets 
packages also have exmaples and widgets built using R tcltk. 

>thanks very much for your help,

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