Hello! I don't know how to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file given by cDNA Agilent Scanner& Sw), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg and annotate pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance! A. S. ---------------------------- |------------------------------------+-------------------------------- ----| |Alessandro Semeria |Tel. +39 544 536811 | |------------------------------------+-------------------------------- ----| |Models and Simulation Laboratory |Fax. +39 544 538663 | |------------------------------------+-------------------------------- ----| |The Environment Research Center - | | |Montecatini (Edison Group), Via | | |Ciro Menotti 48, |E-mail: asemeria@cramont.it | |48023 Marina di Ravenna (RA), Italy | | |------------------------------------+-------------------------------- ----|

You probably need to parse two files to get the mappings you want. One of the file (ftp://ftp.ncbi.nih.gov/refseq/locuslink/LL_tmpl.gz) from LocusLink contains mappings from GenBank Accession numbers to GO ids. Another is the file from GO (ftp://ftp.geneontology.org/pub/go/xml/go_200211_termdb.xml.gz) that contains GO terminologies. I would suggest that you create a ";" separated text file with one column for GenBank names and another for GenBank Accession Numbers. Then, write a segment of Perl script and parse LL_tmpl.gz using AnnBuilder (following the examples in the vignette - Basic functions of AnnBuilder). That will give you the mappings from GenBank names to GO ids. AnnBuilder already have a parser (GOMXLParser) to parser the GO file (Code examples in the vignette - Source specific functions of AnnBuilder). What you need to do then is just to map the GO ids to GO terms. >To: bioconductor@stat.math.ethz.ch >From: AlessandroSemeria@cramont.it >X-MIMETrack: Serialize by Router on ecom/twd(Release 5.0.6a |January 17, 2001) at 12/19/2002 09:36:25 AM >MIME-Version: 1.0 >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=2.1 required=5.0 tests=NO_REAL_NAME,SPAM_PHRASE_00_01 version=2.43 >X-Spam-Level: ** >Subject: [BioC] o >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.0.13 >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >Date: Thu, 19 Dec 2002 09:38:13 +0100 > >Hello! >I don't know how >to associate ontology to a long list of GeneBank Name (a txt-tab file or >an XML file given >by cDNA Agilent Scanner& Sw), i.e. >I would as output a formatted file with 4 columns (1:GeneBank Name >2,3,4:ontology). >I know that I have to perform a mapping of genes, I got a look on >AnnBuilder pkg and annotate pkg, >but I 've not idea from where to start. >Some suggestion? Thanks in advance! > >A. S. > >---------------------------- > >|------------------------------------+------------------------------- -----| >|Alessandro Semeria |Tel. +39 544 536811 | >|------------------------------------+------------------------------- -----| >|Models and Simulation Laboratory |Fax. +39 544 538663 | >|------------------------------------+------------------------------- -----| >|The Environment Research Center - | | >|Montecatini (Edison Group), Via | | >|Ciro Menotti 48, |E-mail: asemeria@cramont.it | >|48023 Marina di Ravenna (RA), Italy | | >|------------------------------------+------------------------------- -----| > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor