Table 1.

Data sources included in JBioWH

Data Type	Data Source	URL	Data Format
Taxonomy	NCBI Taxonomy	ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz	Delim. Text
Ontology	GO	ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-full/	OBO XML
Gene	Gene	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/	Delim. Text
Gene	KEGG Gene	http://www.bioinformatics.jp/en/keggftp.html	Text
Gene	GeneBank	ftp://ftp.ncbi.nih.gov/genbank	Text
Gene	RefSeq	ftp://ftp.ncbi.nih.gov/refseq/release/	Text
Chromosome	Genomes	ftp://ftp.ncbi.nih.gov/genomes/	Delim. Text
Protein	UniProt	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/	XML
Enzyme	KEGG Enzyme	http://www.bioinformatics.jp/en/keggftp.html	Text
PPI	IntAct	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/pmidMIF25.zip	PSI 25 XML
PPI	MINT	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmids/	PSI 25 XML
PPI	DIP	http://dip.doe-mbi.ucla.edu/dip/	PSI 25 XML
PPI	BioGrid	http://thebiogrid.org/	PSI 25 XML
Prot. Cluster	UniRef	ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/	XML
Drug	DrugBank	http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip	XML
Drug	KEGG Comp.	http://www.bioinformatics.jp/en/keggftp.html	Text
Pathway	KEGG Pathway	http://www.bioinformatics.jp/en/keggftp.html	Text
Reaction	KEGG Reaction	http://www.bioinformatics.jp/en/keggftp.html	Text
Disease	OMIM	http://www.omim.org/downloads	Text
Prot. Domain	PFAM	ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam26.0/database_files/	SQL

The databases were accessed in October 2012.