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Question: How to access Emsembl plants with biomaRt
3
gravatar for naholi.alejandri
2.7 years ago by
Mexico
naholi.alejandri40 wrote:

Hello I have updated biomaRt and now I can not find a way to access ENSEMBL_PLANTS mart.

library(biomaRt)
listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=es_MX.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_MX.UTF-8        LC_COLLATE=es_MX.UTF-8    
 [5] LC_MONETARY=es_MX.UTF-8    LC_MESSAGES=es_MX.UTF-8   
 [7] LC_PAPER=es_MX.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.26.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.4        parallel_3.2.2       DBI_0.3.1           
 [4] RCurl_1.95-4.7       Biobase_2.30.0       AnnotationDbi_1.32.0
 [7] RSQLite_1.0.0        S4Vectors_0.8.3      BiocGenerics_0.16.1 
[10] stats4_3.2.2         bitops_1.0-6         XML_3.98-1.3

 

Before there were around 60 options, I have browsed thru this 5 but I can't find ENSEMBL_PLANTS.

Please Help.

Thanks. 

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by naholi.alejandri40
4
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I think it is at

> listMarts(host="plants.ensembl.org")
            biomart              version
1       plants_mart           Plant Mart
2 plants_variations Plant Variation Mart

Previously, the default host was biomart.org which served to federate many different marts. biomart.org is currently unavailable and the host has been changed to ensembl.org. I arrived at plants.ensembl.org by surfing the web for "ensembl plant mart" and looking at the url; not very sophisticated.

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Martin Morgan ♦♦ 22k

Thank you very much , now, I think, I must change several scripts with the plants.ensembl.org host. You saved my day.

ADD REPLYlink written 2.7 years ago by naholi.alejandri40
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