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Growth of Life Science Databases and Semantic Web Technologies

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Mitsuteru Nakao
Mitsuteru Nakao

The document discusses the growth of biological databases and transition to storing data in RDF format. It describes several databases including DDBJ, PDBj, and UniProt that have adopted RDF and the benefits this provides by linking data. It also discusses tools for working with RDF data and challenges in developing semantic web technologies for life science data.

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2011-02-28 JSBi 1 11 3 2 1
DDBJ 1,000 1 http://www.ddbj.nig.ac.jp/images/breakdown_stats/DBGrowth-e.gif 11 3 2 2
20000000.00 15000000.00 10000000.00 2,063 5000000.00 0 1965 1969 1973 1977 1981 1985 1989 1993 1997 2001 2005 2009 http://www.nlm.nih.gov/bsd/index_stats_comp.html 11 3 2 3
10,000 300 2,000 11 3 2 4
lifesciencedb.jp 11 3 2 5
lifesciencedb.jp 11 3 2 6
11 3 2 7
DB 11 3 2 8
11 3 2 9
11 3 2 10
11 3 2 11
11 3 2 12
11 3 2 13
http://togotv.dbcls.jp/20101026.html#p01 11 3 2 14
11 3 2 15
BioHackathon 2008,2009,2010 11 3 2 16
http://motdb.dbcls.jp/ 11 3 2 17
TV TogoTV.dbcls.jp 11 3 2 18
TogoDB.dbcls.jp 11 3 2 19
http://togodb.dbcls.jp/TBA/ 11 3 2 20
11 3 2 21
TogoWS.dbcls.jp /entry/ncbi-pubmed/20727200 /entry/ncbi-pubmed/20727200/abstract /entry/ebi-uniprot/P53_HUMAN 11 3 2 22
http://lifesciencedb.jp/cc/ 11 3 2 23
11 3 2 24
11 3 2 25
11 3 2 26
Web 11 3 2 27
11 3 2 28
11 3 2 29
11 3 2 30
ADNI Alzheimer’s Disease Neuroimaging Initiative http://adni.loni.ucla.edu/ 11 3 2 31
• • • • • 11 3 2 32
http://www.nature.com/ng/journal/v41/n10/full/ng1009-1045.html 11 3 2 33
Sege bionetworks http://www.sagebase.org/ 11 3 2 34
11 3 2 35
↑ ↓ 11 3 2 36
11 3 2 37
11 3 2 38
11 3 2 39
ID 11 3 2 40
P53_HUMAN 11 3 2 41
20727200 11 3 2 42
11 3 2 43
11 3 2 44
Web 11 3 2 45
11 3 2 46
http://www.w3.org/2007/Talks/0130-sb-W3CTechSemWeb/#(24) 11 3 2 47
11 3 2 48
11 3 2 49
Unicode 11 3 2 50
ASCII 11 3 2 51
URI 11 3 2 52
ID URI 11 3 2 53
11 3 2 54
http://www.uniprot.org/uniprot/P29965 http://www.ncbi.nlm.nih.gov/pubmed/20727200 11 3 2 55
RDF 11 3 2 56
Resource Description Framework 11 3 2 57
Subject-Predicate-Object 11 3 2 58
11 3 2 59
11 3 2 60
OWL 11 3 2 61
11 3 2 62
SPARQL 11 3 2 63
11 3 2 64
RDF 11 3 2 65
RSS 11 3 2 66
11 3 2 67
→ 11 3 2 68
UniProt 11 3 2 69
2007 RDF http://dev.isb-sib.ch/projects/uniprot-rdf/ 11 3 2 70
• UniProt • • •→ 11 3 2 71
• RDF • • RDF 11 3 2 72
http://dev.isb-sib.ch/projects/uniprot-rdf/intro.html 11 3 2 73
11 3 2 74
OWL http://dev.isb-sib.ch/projects/uniprot-rdf/owl/ 11 3 2 75
11 3 2 76
11 3 2 77
11 3 2 78
Protein citation Citation Annotation 11 3 2 79
11 3 2 80
11 3 2 81
XML RDF/XML 2.7GB 6.0GB 7.7GB 0.5GB 0.6GB 0.7GB 11 3 2 82
DDBJ RDF 11 3 2 83
• DDBJ • unirprot • 11 3 2 84
PDBj RDF 11 3 2 85
• PDBj • • RDF • PDBj XML RDF/XML 11 3 2 86
RDF DDBJ 299 300GB 6.6G PDBj 65378 133GB 1.4G MEDLINE 617 12GB 0.7G UniProt 12 133GB 2.4G 2010/06 11 3 2 87
RDF 11 3 2 88
LInked Life Data 11 3 2 89
http://linkedlifedata.com/about 11 3 2 90
RDF CSV JSON XML RDF 11 3 2 91
11 3 2 92
BBC Web http://www.bbc.co.uk/blogs/bbcinternet/2010/07/ bbc_world_cup_2010_dynamic_sem.html 11 3 2 93
11 3 2 94
11 3 2 95
11 3 2 96
URI URI 11 3 2 97
Linked Data 11 3 2 98
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/” 11 3 2 99
11 3 2 100
RDF 11 3 2 101
11 3 2 102
11 3 2 103
11 3 2 104
11 3 2 105
11 3 2 106
11 3 2 107
• CC-BY, CC-BY-SA • CC0, Public Domain • Panton • http://pantonprinciples.org/ • attribution citation 11 3 2 108
• Google Refine • Protégé • Virtuoso • Freebase.org • 4store • TogoWS REST API • Sesame • BigOWLIM 11 3 2 109
RDF • Semantic-Systems-Biology.org • Bio2RDF • NeuroCommons • Linked Life Data • LinkDB 11 3 2 110
http://www.oreilly.co.jp/books/9784873114521/ 11 3 2 111
11 3 2 112
• • 2003 NSF 11 3 2 113
11 3 2 114
11 3 2 115
11 3 2 116
11 3 2 117
11 3 2 118
11 3 2 119
11 3 2 120
11 3 2 121
Bioconductor 11 3 2 122
Galaxy 11 3 2 123
Cytoscape 11 3 2 124
BioMart 11 3 2 125
11 3 2 126
11 3 2 127
11 3 2 128
↑ ↓ 11 3 2 129
Galaxy 11 3 2 130
http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter 11 3 2 131
11 3 2 132
Devil in the details, Nature 470, 305-6, 17 Feb. 2011 doi:10.1038/470305b http://www.nature.com/nature/journal/v470/n7334/full/470305b.html 11 3 2 133

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