Dear Jack, You are right, the problem was that columns contained the string 'NULL'. Thanks!
After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do? Thanks! Isaac 2011/8/26 Jack Hsu <[email protected]> > Hi Isaac, > > BioMart displays "no data" when an empty string or NULL value is retrieved. > > Can you check that the column value is NULL instead of the string 'NULL'? > > > Cheers, > > -jack > > > From: Isaac cano <[email protected]> > Date: Fri, 26 Aug 2011 03:47:02 -0400 > To: BioMart Users <[email protected]> > Subject: [BioMart Users] linkouturl for an attribute with no data > > Dear BioMart users, > > In our local database we store the PubMed IDs of experiments and we use the > linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set > a link for this attribute in the query results that links with the > corresponding article in PubMed. It is the case that we have experiments > with no PubMed IDs so in the query results we still get a link that if the > attribute in the database is NULL by default the link is like > NULL<http://www.ncbi.nlm.nih.gov/pubmed?term=NULL> > . > > I've seen that for example Ensembl present a "no data" value for those > cases were actually there is no data but in this case the link is disabled. > Is there a way to tell to BioMart not to create a link for attributes with > no data ? > > Thanks in advance, > > -- > Isaac Cano > Bioinformatics > Linkcare Health Services SL > C/Villarroel 170 > 08036 - Barcelona > Tel.: (+34)932 275 400, ext. 4182\4523 > Mobile: (+34) 666 186 748 > Fax: (+34) 932 275 455 > [email protected] > > -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]
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