In this case, it looks like a pointer problem. Junjun: I believe Marie reported the same problem to you a few months ago. Marie do you want to shed some light on it? Junjun: please confirm that this indeed the same problem and let us know if you made any progress on fxing that?
a On Thu, Sep 1, 2011 at 10:42 AM, Isaac cano <[email protected]> wrote: > 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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