This problem has been resolved. Your query should now return the expected results.
On 2011-03-03, at 9:41 AM, Jonathan Guberman wrote: Holger, We try to keep biomart.org<http://biomart.org/> in sync with our sources, and we announce updates on this list. In fact, biomart.org<http://biomart.org/> IS synchronized to the current version of Ensembl, and when I check the underlying database they are indeed in agreement (i.e., it returns two transcripts). However, for some reason the web service is only returning the one result. So, you seem to have uncovered a bug. Thank you for reporting it, and we'll post to the list when the cause has been determined and it has been fixed. Jonathan Guberman, PhD Application Programmer Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7818 Toll-free: 1-866-678-6427 www.oicr.on.ca<http://www.oicr.on.ca/> On 2011-03-03, at 4:28 AM, Holger Brandl wrote: Hi, I'm using the biomaRt package in R to query gene transcripts from "Ensembl Genes 61; Mus Musculus NCBIM37". Unfortunately I obtain different results depending on which biomart-service I'm using. Here's an example: defaultMart = useDataset("mmusculus_gene_ensembl", mart = useMart("ensembl")) ensemblMart <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "www.ensembl.org<http://www.ensembl.org/>", path = "/biomart/martservice", archive = FALSE) getBM(attributes=c('ensembl_gene_id', 'ensembl_transcript_id'), filters=c('ensembl_gene_id'), values=c('ENSMUSG00000047507'),mart=defaultMart); ensembl_gene_id ensembl_transcript_id 1 ENSMUSG00000047507 ENSMUST00000056357 getBM(attributes=c('ensembl_gene_id', 'ensembl_transcript_id'), filters=c('ensembl_gene_id'), values=c('ENSMUSG00000047507'),mart=ensemblMart); ensembl_gene_id ensembl_transcript_id 1 ENSMUSG00000047507 ENSMUST00000056357 2 ENSMUSG00000047507 ENSMUST00000169109 So obviously one transcript is missing when using the default mart. It looks to me that the biomart-service is not in sync with ensembl, because if I use the archive mirror 'nov2010.archive.ensembl.org' the ensembl results match the biomart.org<http://biomart.org/> results. Is there a sync-schedule available? Or is there another reason for the mismatch? Best, Holger Brandl -- Dr. Holger Brandl Bioinformatics Service Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 Dresden, Germany Tel.: +49/351/210-2738 Fax: +49 351 210 2000 www: http://www.mpi-cbg.de<http://www.mpi-cbg.de/> _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users <ATT00002..txt>
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