Hi Isaac, We discussed this over here. If we understand your use case correctly it is similar to what Marie tried to do, both queries involve more than two datasets join. Marie was able to find a suitable dataset that contains enough information that she needed and avoided three datasets join.
Three datasets join works under certain situations. The following query involves: pathway dataset from reactome, gene dataset and sample dataset. <!DOCTYPE Query> <Query client="true" processor="TSV" limit="-1" header="1"> <Dataset name="hsapiens_gene_ensembl_hopkinsColon" config="gene_ensembl_config"> <Filter name="_displayname" value="ABC-family proteins mediated transport"/> <Attribute name="hsapiens_gene_ensembl__simple_somatic_mutation__dm__tumour_sample_id"/> <Attribute name="hsapiens_gene_ensembl__simple_somatic_mutation__dm__mutation_id"/> <Attribute name="hsapiens_gene_ensembl__simple_somatic_mutation__dm__mutation"/> <Attribute name="hsapiens_gene_ensembl__simple_somatic_mutation__dm__mutation_type"/> <Attribute name="sample__sample__main__donor_id"/><Attribute name="cancertype"/> <Attribute name="assemblyversion"/><Attribute name="ensembl_gene_id"/> <Attribute name="ensembl_transcript_id"/> <Attribute name="external_gene_id"/> </Dataset> </Query> The linking between pathway and gene datasets is ensembl_gene_id, and sample_id is used to link gene and sample datasets. The query is fired against gene dataset which includes filterPointer to pathway and attributePointers to sample. If you can configure it in similar way, your query should work. You can open icgc6.xml configuration file to figure out how it's done. Hope this helps, Kind regards, Junjun From: Isaac cano <[email protected]<mailto:[email protected]>> Date: Thu, 1 Sep 2011 10:58:21 -0400 To: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Cc: BioMart Users <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] linkouturl for an attribute with no data 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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Fri, 26 Aug 2011 03:47:02 -0400 To: BioMart Users <[email protected]<mailto:[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<tel:%28%2B34%29932%20275%20400%2C%20ext.%204182>\4523 Mobile: (+34) 666 186 748<tel:%28%2B34%29%20666%20186%20748> Fax: (+34) 932 275 455<tel:%28%2B34%29%20932%20275%20455> [email protected]<mailto:[email protected]> -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182<tel:%28%2B34%29932%20275%20400%2C%20ext.%204182>\4523 Mobile: (+34) 666 186 748<tel:%28%2B34%29%20666%20186%20748> Fax: (+34) 932 275 455<tel:%28%2B34%29%20932%20275%20455> [email protected]<mailto:[email protected]> _______________________________________________ Users mailing list [email protected]<mailto:[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<tel:%28%2B34%29932%20275%20400%2C%20ext.%204182>\4523 Mobile: (+34) 666 186 748<tel:%28%2B34%29%20666%20186%20748> Fax: (+34) 932 275 455<tel:%28%2B34%29%20932%20275%20455> [email protected]<mailto:[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]<mailto:[email protected]>
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