Thanks Arek, Marie and Junjun for checking this problem! I hope there is a solution!
Thanks again! Isaac 2011/9/1 Arek Kasprzyk <[email protected]> > 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] >> >> > -- 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
