[biomart-users] About athaliana_eg_gene Attributes

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[biomart-users] About athaliana_eg_gene Attributes

Roxy J
Hi,

I am using biomart for Athaliana plant and i am having a hard time finding the attribute that goes with my GetBM() function.  I have 
ibrary("biomaRt") listMarts(host="plants.ensembl.org") # To choose BioMart database m <- useMart("plants_mart", host="plants.ensembl.org"); listDatasets(m) m <- useMart("plants_mart", host="plants.ensembl.org", dataset="athaliana_eg_gene") listAttributes(m) # Choose data types you want to download go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)

And it is saying that i am using the wrong Attributes (go_accession, go_namespace_1003) no complaint for "tair_locus".


can anyboby tell me what i am doing wrong?

Thanks,

Roxy

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Re: [biomart-users] About athaliana_eg_gene Attributes

Syed Haider-5
Hi Roxy,

The attributes you have specified do not exist in the current version of Ensembl Plants -  i think!
Here is a list of currently valid list of GO attributes in Ensembl Plants, so you may have to use one of these:

	<Attribute name = "go_id" />
	<Attribute name = "name_1006" />
	<Attribute name = "definition_1006" />
	<Attribute name = "go_linkage_type" />
	<Attribute name = "namespace_1003" />
	<Attribute name = "goslim_goa_accession" />
	<Attribute name = "goslim_goa_description" />

Hope this helps,
Syed


On 22 August 2017 at 20:15, Roxy J <[hidden email]> wrote:
Hi,

I am using biomart for Athaliana plant and i am having a hard time finding the attribute that goes with my GetBM() function.  I have 
ibrary("biomaRt") listMarts(host="plants.ensembl.org") # To choose BioMart database m <- useMart("plants_mart", host="plants.ensembl.org"); listDatasets(m) m <- useMart("plants_mart", host="plants.ensembl.org", dataset="athaliana_eg_gene") listAttributes(m) # Choose data types you want to download go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)

And it is saying that i am using the wrong Attributes (go_accession, go_namespace_1003) no complaint for "tair_locus".


can anyboby tell me what i am doing wrong?

Thanks,

Roxy

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Re: [biomart-users] About athaliana_eg_gene Attributes

Thomas Maurel
Dear Roxy,

Syed is right, we moved to a new system in EG release 35 to generate and populate the marts filters/attributes. As a result, we have improved the consistency of our mart across the vertebrate and other ensembl divisions. You can find the full list of changes on the EG 35 FTP site: ftp://ftp.ensemblgenomes.org/pub/release-35/release_35_biomart_changes.txt

Apologies for any inconvenience caused.
Kind Regards,
Thomas
On 23 Aug 2017, at 10:25, Syed Haider <[hidden email]> wrote:

Hi Roxy,

The attributes you have specified do not exist in the current version of Ensembl Plants -  i think!
Here is a list of currently valid list of GO attributes in Ensembl Plants, so you may have to use one of these:

	<Attribute name = "go_id" />
	<Attribute name = "name_1006" />
	<Attribute name = "definition_1006" />
	<Attribute name = "go_linkage_type" />
	<Attribute name = "namespace_1003" />
	<Attribute name = "goslim_goa_accession" />
	<Attribute name = "goslim_goa_description" />

Hope this helps,
Syed


On 22 August 2017 at 20:15, Roxy J <[hidden email]> wrote:
Hi,

I am using biomart for Athaliana plant and i am having a hard time finding the attribute that goes with my GetBM() function.  I have 
ibrary("biomaRt") listMarts(host="plants.ensembl.org") # To choose BioMart database m <- useMart("plants_mart", host="plants.ensembl.org"); listDatasets(m) m <- useMart("plants_mart", host="plants.ensembl.org", dataset="athaliana_eg_gene") listAttributes(m) # Choose data types you want to download go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)

And it is saying that i am using the wrong Attributes (go_accession, go_namespace_1003) no complaint for "tair_locus".


can anyboby tell me what i am doing wrong?

Thanks,

Roxy

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] About athaliana_eg_gene Attributes

Roxy J
Thanks Thomas and Syed! That solves the problem.

Roxy

Sent from my iPhone

On Aug 23, 2017, at 4:38 AM, Thomas Maurel <[hidden email]> wrote:

Dear Roxy,

Syed is right, we moved to a new system in EG release 35 to generate and populate the marts filters/attributes. As a result, we have improved the consistency of our mart across the vertebrate and other ensembl divisions. You can find the full list of changes on the EG 35 FTP site: ftp://ftp.ensemblgenomes.org/pub/release-35/release_35_biomart_changes.txt

Apologies for any inconvenience caused.
Kind Regards,
Thomas
On 23 Aug 2017, at 10:25, Syed Haider <[hidden email]> wrote:

Hi Roxy,

The attributes you have specified do not exist in the current version of Ensembl Plants -  i think!
Here is a list of currently valid list of GO attributes in Ensembl Plants, so you may have to use one of these:

	<Attribute name = "go_id" />
	<Attribute name = "name_1006" />
	<Attribute name = "definition_1006" />
	<Attribute name = "go_linkage_type" />
	<Attribute name = "namespace_1003" />
	<Attribute name = "goslim_goa_accession" />
	<Attribute name = "goslim_goa_description" />

Hope this helps,
Syed


On 22 August 2017 at 20:15, Roxy J <[hidden email]> wrote:
Hi,

I am using biomart for Athaliana plant and i am having a hard time finding the attribute that goes with my GetBM() function.  I have 
ibrary("biomaRt") listMarts(host="plants.ensembl.org") # To choose BioMart database m <- useMart("plants_mart", host="plants.ensembl.org"); listDatasets(m) m <- useMart("plants_mart", host="plants.ensembl.org", dataset="athaliana_eg_gene") listAttributes(m) # Choose data types you want to download go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)

And it is saying that i am using the wrong Attributes (go_accession, go_namespace_1003) no complaint for "tair_locus".


can anyboby tell me what i am doing wrong?

Thanks,

Roxy

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You received this message because you are subscribed to the Google Groups "biomart-users" group.
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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