[biomart-users] Finding different species from Phytozome with biomaRt

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[biomart-users] Finding different species from Phytozome with biomaRt

Alistair Leverett
Hello,
 I have been struggling to use biomart in R to retrieve info from a variety of plant species. I have done the following :

> options(RCurlOptions=list(followlocation=TRUE, postredir=2L))
> phytozome <- useMart('phytozome_mart', host="phytozome.jgi.doe.gov", path ="/biomart/martservice/", dataset = 'phytozome')
> t2f <- getBM(attributes = c("ortholog_group","ortholog__dm_gene_name","ortholog__dm_organism_name", "ortholog__dm_ortholog_gene_name"),filters= c("organism_id"), values = c(382), mart = phytozome)    

However I have a problem. This gives me data from K. laxiflora, which is specified by the argument values =c(382) in the third line. If I want to download data from another species, how would i do this? So far my only approach has been to use trial and error to work out which value corresponds to which species (i.e. change the number which i am setting for value). But this is very laborious. I would like to know if there is a way of viewing which value corresponds to which species? So far i cannot find any way to view this.

Any help will be much appreciated

best wishes
Ali

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[biomart-users] Re: Finding different species from Phytozome with biomaRt

joe carlson
Hello Ali,

This question is not so much an issue with biomart, but a detail of our implementation and data model.

Our biomart database includes different versions of the genome and annotation for some organisms. So we cannot use the organism name as a unique key for the data set. We use a unique integer key to designate the particular annotation. This is represented in biomart as the organism_id.

I see the source of your problem: we use the organism_id internally when making queries, but we do not expose it. Nor do we have a simple organism name filter in place that you can use. I'll work on this for the next deployment of our biomart. In the mean time, here is how you can get a lookup list of organism id and organism names in our biomart: 

https://phytozome.jgi.doe.gov/phytomine/service/query/results?query=%3Cquery+name%3D%22%22+model%3D%22genomic%22+view%3D%22Organism.proteomeId+Organism.shortName+Organism.version%22+longDescription%3D%22%22+sortOrder%3D%22Organism.proteomeId+asc%22%3E%3C%2Fquery%3E&format=tab

(yes. It's an intermine query. I hope I will be forgiven for posting the link on this list.)


On Tuesday, October 18, 2016 at 10:57:11 AM UTC-7, Alistair Leverett wrote:
Hello,
 I have been struggling to use biomart in R to retrieve info from a variety of plant species. I have done the following :

> options(RCurlOptions=list(followlocation=TRUE, postredir=2L))
> phytozome <- useMart('phytozome_mart', host="<a href="http://phytozome.jgi.doe.gov" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;">phytozome.jgi.doe.gov", path ="/biomart/martservice/", dataset = 'phytozome')
> t2f <- getBM(attributes = c("ortholog_group","ortholog__dm_gene_name","ortholog__dm_organism_name", "ortholog__dm_ortholog_gene_name"),filters= c("organism_id"), values = c(382), mart = phytozome)    

However I have a problem. This gives me data from K. laxiflora, which is specified by the argument values =c(382) in the third line. If I want to download data from another species, how would i do this? So far my only approach has been to use trial and error to work out which value corresponds to which species (i.e. change the number which i am setting for value). But this is very laborious. I would like to know if there is a way of viewing which value corresponds to which species? So far i cannot find any way to view this.

Any help will be much appreciated

best wishes
Ali

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