A script to create a BrigdeDb database from BioMart queries.
In your terminal:
java -jar BioMart2BridgeDb.jar <configFile> <outputPath> <oldDB> <inclusive>
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<configFile>: location of configuration file
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<outputPath>: Path for the new database
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<oldDB>: (optional) directory of the old database - run QC
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<inclusive>: (optional) use inclusive BridgeDb list
Example: Danio rerio config file
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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/
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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
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Code name of the species: http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL
species=athaliana_eg_gene
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The name of the bridge database
database_name=Arabidopsis thaliana genes and proteins
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The name of the file .bridge created
file_name=At_Derby_Ensembl_Plant_28
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The different data source code name can be found like there:
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
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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