Hi Zhining, biomaRt package relies on BioMart REST API, it works with the current BioMart central portal and others that run BioMart release 0.7. ICGC Data Portal runs off BioMart 0.8 release candidate 6 which does not provide 0.7 compatible REST API at this time, so it will not work even you specify ICGC's URL while using biomaRt.
This is actually a good timing, we are planning to standardize REST API in 0.8. I hope biomaRt will work with data sources that run BioMart 0.8 software in the near future. Cheers, Junjun From: "Wang, Zhining (NIH/NCI) [C]" <[email protected]<mailto:[email protected]>> Date: Mon, 1 Aug 2011 12:38:50 -0400 To: jzhang <[email protected]<mailto:[email protected]>> Subject: FW: [BioMart Users] About connection to ICGC data portal Hi Junjun, Sorry to bother you again. What is the URL for the ICGC web service that biomaRt can connect to? Steffen told me that I could use the URL directly to establish connection through biomaRt. e.g. Ensembl can be queried by doing: listMarts(host="may2009.archive.ensembl.org<http://may2009.archive.ensembl.org>") mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org<http://may2009.archive.ensembl.org>") Thanks, Zhining From: Steffen Durinck [mailto:[email protected]] Sent: Monday, August 01, 2011 12:23 PM To: Wang, Zhining (NIH/NCI) [C] Cc: [email protected]<mailto:[email protected]> Subject: Re: [BioMart Users] About connection to ICGC data portal Hi Zhining, By default, biomaRt queries the central BioMart server. ICGC is not hosted there. If you know the host of the ICGC web service URL you could use that directy to establish your connection through biomaRt. e.g. Ensembl can be queried through the central BioMart service but also by doing: listMarts(host="may2009.archive.ensembl.org<http://may2009.archive.ensembl.org>") mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='hsapiens_gene_ensembl', host="may2009.archive.ensembl.org<http://may2009.archive.ensembl.org>") Cheers, Steffen On Mon, Aug 1, 2011 at 6:05 AM, Wang, Zhining (NIH/NCI) [C] <[email protected]<mailto:[email protected]>> wrote: Hi, I am playing with the R package, BiomaRt. I tried library("biomaRt"); listMarts(); It returned 66 Mart, but I can not find the Mart for ICGC which is powered by BioMart (http://dcc.icgc.org/). Can you help? Thanks, Zhining Zhining Wang, Ph. D. Senior Scientist, Bioinformatics SRA International, Inc. Contractor, TCGA program office, NCI/NIH Bethesda, Maryland Building31A, room 3A20 Tel: 301-435-0680<tel:301-435-0680> Email: [email protected]<mailto:[email protected]> _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
