BioMartScript

Introduction

A script to create a BrigdeDb database from BioMart queries.

Run

In your terminal:

java -jar BioMart2BridgeDb.jar <configFile> <outputPath> <oldDB> <inclusive>

• <configFile>: location of configuration file

• <outputPath>: Path for the new database

• <oldDB>: (optional) directory of the old database - run QC

• <inclusive>: (optional) use inclusive BridgeDb list

List of default config files:

https://github.com/JonathanMELIUS/BioMartScript/tree/bc62ed7fba16dd143292ee10fb4e261d196dd7a6/src/resource

Example: Danio rerio config file

How to create your own config file

• Give the version of Ensembl BioMart to query:

  e.g: http://www.ensembl.org/biomart/, http://oct2014.archive.ensembl.org/biomart/, http://metazoa.ensembl.org/biomart/

  endpoint=http://plants.ensembl.org/biomart/

• MartRegistry can be found there:

  http://plants.ensembl.org/biomart/martservice?type=registry

  e.g: protists_mart_27, metazoa_mart_27, default

  schema=plants_mart_27

• Code name of the species: http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL

  species=athaliana_eg_gene

• The name of the bridge database

  database_name=Arabidopsis thaliana genes and proteins

• The name of the file .bridge created

  file_name=At_Derby_Ensembl_Plant_28

• The different data source code name can be found like there:

  http://plants.ensembl.org/biomart/martservice?type=attributes&mart=plants_mart_27&dataset=athaliana_eg_gene

  probe_set=affy_ath1_121501 gene_datasource=refseq_mrna,refseq_ncrna,refseq_peptide,uniprot_sptrembl,pdb,tair_locus,go_accession,unigene,entrezgene,wikigene_id,nasc_gene_id,uniprot_swissprot_accession

• Optional filters (chromosome list)

  e.g: chromosome_name=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,X,MT

  http://may2015.archive.ensembl.org/biomart/martservice?type=filters&dataset=btaurus_gene_ensembl