Hi Isaac, to define the problem better ei to find out if this is data related or software related problem I suggest you do the following:
1. get ensembl <-> reactome set (through ensembl id) 2. get local <-> ensembl (through affy id) then manually see if there is an intersection between those sets? If there is this is a software problem, if not it is a data problem I hope i understood your linking correctly :) a. On Thu, Sep 1, 2011 at 9:47 AM, Isaac cano <[email protected]> wrote: > 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] > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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