Triple Store Survey for Life Science Data

• Overview
• Platform
• Data
• Database
  • Bigdata => Bigdata
  • 4store => 4store
  • Virtuoso => Virtuoso
  • Owlim-se => OwlimSe
  • Mulgara => Mulgara

Overview

Platform

* Machine:

• OS: GNU/linux
• CPU: GenuineIntel? 6; model name : Intel(R) Xeon(R) CPU E5649 @ 2.53GHz; 12 cores 24 hyper-threading
• Mem: 65996128 kB
• Harddisk: SCSI Raid 0 (three hard disks of 1 Tera bytes, two of them are used to store data)

* Software:

• JDK:1.6.0_26
• Virtuoso: 6.3 commercial
• OwlimSE: 4.3.4238
• Mulgara: 2.1.12
• 4store: 1.1.4
• Bigdata: RWSTORE_1_1_0

Data

Allie: .n3 format, 94,420,989 tripples, sparql query attachment:allie.txt .

PDBJ: .rdf.gz format ,589,987,335 triples, 77878 files, from  ftp://ftp.pdbj.org/XML/rdf/. sparql query attachment:pdbj.txt .

Uniprot: .rdf.gz format , about 4 billion triples, the 3 largest files are uniprot.rdf.gz,uniparc.rdf.gz,uniref.rdf.gz, from  ftp://ftp.uniprot.org/pub/databases/uniprot/ (the experiment used data was 2011.Nov version). sparql query attachment:uniprot.txt or  http://beta.sparql.uniprot.org/.

DDBJ: .rdf.gz format, about 8 billion triples, 330 files, from  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/. sparql query attachment:ddbj.txt .