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データ統合とサイバーインフラストラクチャ
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データ統合とサイバーインフラストラクチャ

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2010/2/28(月) JSBi 第1回 応用システムバイオロジー研究会 …

2010/2/28(月) JSBi 第1回 応用システムバイオロジー研究会
http://togodb.dbcls.jp/TBA/

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  • 1. 2011-02-28 JSBi 111 3 2 1
  • 2. DDBJ 1,000 1 http://www.ddbj.nig.ac.jp/images/breakdown_stats/DBGrowth-e.gif11 3 2 2
  • 3. 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.html11 3 2 3
  • 4. 10,000 300 2,00011 3 2 4
  • 5. lifesciencedb.jp11 3 2 5
  • 6. lifesciencedb.jp11 3 2 6
  • 7. 11 3 2 7
  • 8. DB11 3 2 8
  • 9. 11 3 2 9
  • 10. 11 3 2 10
  • 11. 11 3 2 11
  • 12. 11 3 2 12
  • 13. 11 3 2 13
  • 14. http://togotv.dbcls.jp/20101026.html#p0111 3 2 14
  • 15. 11 3 2 15
  • 16. BioHackathon 2008,2009,201011 3 2 16
  • 17. http://motdb.dbcls.jp/11 3 2 17
  • 18. TV TogoTV.dbcls.jp11 3 2 18
  • 19. TogoDB.dbcls.jp11 3 2 19
  • 20. http://togodb.dbcls.jp/TBA/11 3 2 20
  • 21. 11 3 2 21
  • 22. TogoWS.dbcls.jp /entry/ncbi-pubmed/20727200 /entry/ncbi-pubmed/20727200/abstract /entry/ebi-uniprot/P53_HUMAN11 3 2 22
  • 23. http://lifesciencedb.jp/cc/11 3 2 23
  • 24. 11 3 2 24
  • 25. 11 3 2 25
  • 26. 11 3 2 26
  • 27. Web11 3 2 27
  • 28. 11 3 2 28
  • 29. 11 3 2 29
  • 30. 11 3 2 30
  • 31. ADNI Alzheimer’s Disease Neuroimaging Initiative http://adni.loni.ucla.edu/11 3 2 31
  • 32. • • • • •11 3 2 32
  • 33. http://www.nature.com/ng/journal/v41/n10/full/ng1009-1045.html11 3 2 33
  • 34. Sege bionetworks http://www.sagebase.org/11 3 2 34
  • 35. 11 3 2 35
  • 36. ↑ ↓11 3 2 36
  • 37. 11 3 2 37
  • 38. 11 3 2 38
  • 39. 11 3 2 39
  • 40. ID11 3 2 40
  • 41. P53_HUMAN11 3 2 41
  • 42. 2072720011 3 2 42
  • 43. 11 3 2 43
  • 44. 11 3 2 44
  • 45. Web11 3 2 45
  • 46. 11 3 2 46
  • 47. http://www.w3.org/2007/Talks/0130-sb-W3CTechSemWeb/#(24)11 3 2 47
  • 48. 11 3 2 48
  • 49. 11 3 2 49
  • 50. Unicode11 3 2 50
  • 51. ASCII11 3 2 51
  • 52. URI11 3 2 52
  • 53. ID URI11 3 2 53
  • 54. 11 3 2 54
  • 55. http://www.uniprot.org/uniprot/P29965 http://www.ncbi.nlm.nih.gov/pubmed/2072720011 3 2 55
  • 56. RDF11 3 2 56
  • 57. Resource Description Framework11 3 2 57
  • 58. Subject-Predicate-Object11 3 2 58
  • 59. 11 3 2 59
  • 60. 11 3 2 60
  • 61. OWL11 3 2 61
  • 62. 11 3 2 62
  • 63. SPARQL11 3 2 63
  • 64. 11 3 2 64
  • 65. RDF11 3 2 65
  • 66. RSS11 3 2 66
  • 67. 11 3 2 67
  • 68. →11 3 2 68
  • 69. UniProt11 3 2 69
  • 70. 2007 RDF http://dev.isb-sib.ch/projects/uniprot-rdf/11 3 2 70
  • 71. • UniProt • • •→11 3 2 71
  • 72. • RDF • • RDF11 3 2 72
  • 73. http://dev.isb-sib.ch/projects/uniprot-rdf/intro.html11 3 2 73
  • 74. 11 3 2 74
  • 75. OWL http://dev.isb-sib.ch/projects/uniprot-rdf/owl/11 3 2 75
  • 76. 11 3 2 76
  • 77. 11 3 2 77
  • 78. 11 3 2 78
  • 79. Protein citation Citation Annotation11 3 2 79
  • 80. 11 3 2 80
  • 81. 11 3 2 81
  • 82. XML RDF/XML 2.7GB 6.0GB 7.7GB 0.5GB 0.6GB 0.7GB11 3 2 82
  • 83. DDBJ RDF11 3 2 83
  • 84. • DDBJ • unirprot •11 3 2 84
  • 85. PDBj RDF11 3 2 85
  • 86. • PDBj • • RDF • PDBj XML RDF/XML11 3 2 86
  • 87. RDF DDBJ 299 300GB 6.6G PDBj 65378 133GB 1.4G MEDLINE 617 12GB 0.7G UniProt 12 133GB 2.4G 2010/0611 3 2 87
  • 88. RDF11 3 2 88
  • 89. LInked Life Data11 3 2 89
  • 90. http://linkedlifedata.com/about11 3 2 90
  • 91. RDF CSV JSON XML RDF11 3 2 91
  • 92. 11 3 2 92
  • 93. BBC Webhttp://www.bbc.co.uk/blogs/bbcinternet/2010/07/ bbc_world_cup_2010_dynamic_sem.html11 3 2 93
  • 94. 11 3 2 94
  • 95. 11 3 2 95
  • 96. 11 3 2 96
  • 97. URI URI11 3 2 97
  • 98. Linked Data11 3 2 98
  • 99. “Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”11 3 2 99
  • 100. 11 3 2 100
  • 101. RDF11 3 2 101
  • 102. 11 3 2 102
  • 103. 11 3 2 103
  • 104. 11 3 2 104
  • 105. 11 3 2 105
  • 106. 11 3 2 106
  • 107. 11 3 2 107
  • 108. • CC-BY, CC-BY-SA • CC0, Public Domain • Panton • http://pantonprinciples.org/ • attribution citation11 3 2 108
  • 109. • Google Refine • Protégé • Virtuoso • Freebase.org • 4store • TogoWS REST API • Sesame • BigOWLIM11 3 2 109
  • 110. RDF • Semantic-Systems-Biology.org • Bio2RDF • NeuroCommons • Linked Life Data • LinkDB11 3 2 110
  • 111. http://www.oreilly.co.jp/books/9784873114521/11 3 2 111
  • 112. 11 3 2 112
  • 113. • • 2003 NSF11 3 2 113
  • 114. 11 3 2 114
  • 115. 11 3 2 115
  • 116. 11 3 2 116
  • 117. 11 3 2 117
  • 118. 11 3 2 118
  • 119. 11 3 2 119
  • 120. 11 3 2 120
  • 121. 11 3 2 121
  • 122. Bioconductor11 3 2 122
  • 123. Galaxy11 3 2 123
  • 124. Cytoscape11 3 2 124
  • 125. BioMart11 3 2 125
  • 126. 11 3 2 126
  • 127. 11 3 2 127
  • 128. 11 3 2 128
  • 129. ↑ ↓11 3 2 129
  • 130. Galaxy11 3 2 130
  • 131. http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter11 3 2 131
  • 132. 11 3 2 132
  • 133. 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.html11 3 2 133