Hello, The information applies to the data itself - whether in the Table browser, direct mySQL queries, or in the text files.
An example is the first row .... mm9.gbCdnaInfo.geneName (via refLink.geneName) What this information is telling you is what key to use to join the two tables together (refLink and gbCdnaInfo). In a mySQL query, this would be in the "where" clause, such as where refLink.geneName = gbCdnaInfo.geneName (I left off the mm9, since both tables are from the same database, but you can include it to have the "full path" if you want or are able to join between databases). For the Table browser, the tables can be linked by choosing output format as "selected fields from primary and related tables. When selected, the list of associated tables comes up as a form where you can check the ones you want to include, submit, then select the actual columns to include. Many cycles of this can be done, depending on the data size. In general, the gbCdna table is pretty large and not recommended for use in the Table browser. Try the mySQL server or the text files in Downloads instead. Other examples and help are here: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/FAQ/FAQdownloads#download29 For mySQL query help, there are several public web sites that offer help. Using "mysql commands" seemed to be a good google query - it bypassed most the commercial/licencing links. We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Peng Yu" <pengyu...@gmail.com> wrote: > From: "Peng Yu" <pengyu...@gmail.com> > To: gen...@soe.ucsc.edu > Sent: Tuesday, December 1, 2009 2:00:02 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] How to use 'Connected Tables and Joining Fields'? > > I'm on the page of 'Schema for refLink' (selected from Table > Browser). > This is a section Connected Tables and Joining Fields, which has the > following information > > mm9.gbCdnaInfo.geneName (via refLink.geneName) > mm9.geneName.id (via refLink.geneName) > mm9.knownToLocusLink.value (via refLink.locusLinkId) > mm9.ccdsInfo.mrnaAcc (via refLink.mrnaAcc) > mm9.gbCdnaInfo.acc (via refLink.mrnaAcc) > mm9.gbSeq.acc (via refLink.mrnaAcc) > mm9.gbStatus.acc (via refLink.mrnaAcc) > mm9.imageClone.acc (via refLink.mrnaAcc) > mm9.kgXref.refseq (via refLink.mrnaAcc) > mm9.knownToRefSeq.value (via refLink.mrnaAcc) > mm9.mrnaOrientInfo.name (via refLink.mrnaAcc) > mm9.refFlat.name (via refLink.mrnaAcc) > mm9.refGene.name (via refLink.mrnaAcc) > mm9.refSeqAli.qName (via refLink.mrnaAcc) > mm9.refSeqStatus.mrnaAcc (via refLink.mrnaAcc) > mm9.refSeqSummary.mrnaAcc (via refLink.mrnaAcc) > mm9.seq.acc (via refLink.mrnaAcc) > visiGene.gene.name (via refLink.name) > mm9.gbCdnaInfo.productName (via refLink.prodName) > mm9.productName.id (via refLink.prodName) > mm9.kgProtAlias.alias (via refLink.protAcc) > mm9.kgSpAlias.alias (via refLink.protAcc) > mm9.kgXref.protAcc (via refLink.protAcc) > mm9.seq.acc (via refLink.protAcc) > > I think that this is to be used with mysql. But I'm not sure how to > use it exactly. Would you please give me some examples? > _______________________________________________ > Genome maillist - Genome@lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
