Hi Arek, I've checked that there is data intersection between ensembl, reactome and our local database like the following:
Ensembl Gene id Affy_id Pathway name ENSG00000047249 221504_s_at Signaling by Insulin receptor ENSG00000047249 221504_s_at Insulin receptor recycling ENSG00000047249 221504_s_at HIV Infection ENSG00000047249 221504_s_at Host Interactions of HIV factors ENSG00000047249 221504_s_at Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters ENSG00000047249 221504_s_at The role of Nef in HIV-1 replication and disease pathogenesis ENSG00000047249 221504_s_at Nef Mediated CD4 Down-regulation ENSG00000047249 221504_s_at Nef Mediated CD8 Down-regulation ENSG00000047249 221504_s_at Transmembrane transport of small molecules ENSG00000047249 221504_s_at Iron uptake and transport ENSG00000047249 221504_s_at Transferrin endocytosis and recycling The local database contains the affy_id, the ensembl gene id comes from ensembl and the pathway name comes from reactome. In this case, the problem should be a software problem I think. Any idea what should be going wrong? Thanks for your help, Isaac 2011/9/1 Arek Kasprzyk <[email protected]> > 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 >> >> > -- 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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