[BioMart Users] Inconsistent results when using different marts

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[BioMart Users] Inconsistent results when using different marts

Holger Brandl
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", 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 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

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Re: [BioMart Users] Inconsistent results when using different marts

Jonathan Guberman
Holger,

We try to keep biomart.org in sync with our sources, and we announce updates on this list. In fact, 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
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

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", 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 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

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


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Re: [BioMart Users] Inconsistent results when using different marts

Jonathan Guberman
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 in sync with our sources, and we announce updates on this list. In fact, 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
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

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", 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 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

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

<ATT00002..txt>


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Re: [BioMart Users] Inconsistent results when using different marts

Holger Brandl
Jonathan,

wow, this was fast! I've tried it and it works perfectly now. :-)

Thank you very much, best,
Holger

On 3/3/11 10:57 PM, Jonathan Guberman wrote:
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 in sync with our sources, and we announce updates on this list. In fact, 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
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

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", 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 results. Is there a sync-schedule available? Or is there another
reason for the mismatch?

Best, Holger Brandl


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users