2011-02-28 JSBi   111   3   2            1
DDBJ 1,000                              1              http://www.ddbj.nig.ac.jp/images/breakdown_stats/DBGrowth-e.gif11  ...
20000000.00             15000000.00             10000000.00                                              2,063            ...
10,000   300                       2,00011   3   2                     4
lifesciencedb.jp11   3   2                      5
lifesciencedb.jp11   3   2                  6
11   3   2   7
DB11   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#p0111   3   2                                          14
11   3   2   15
BioHackathon               2008,2009,201011   3   2                      16
http://motdb.dbcls.jp/11   3   2                            17
TV   TogoTV.dbcls.jp11   3   2                      18
TogoDB.dbcls.jp11   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             /entr...
http://lifesciencedb.jp/cc/11   3   2                                 23
11   3   2   24
11   3   2   25
11   3   2   26
Web11   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...
•             •             •             •             •11   3   2       32
http://www.nature.com/ng/journal/v41/n10/full/ng1009-1045.html11   3   2                                                  ...
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
ID11   3   2        40
P53_HUMAN11   3   2               41
2072720011   3   2              42
11   3   2   43
11   3   2   44
Web11   3   2         45
11   3   2   46
http://www.w3.org/2007/Talks/0130-sb-W3CTechSemWeb/#(24)11   3   2                                                        ...
11   3   2   48
11   3   2   49
Unicode11   3   2             50
ASCII11   3   2           51
URI11   3   2         52
ID   URI11   3   2              53
11   3   2   54
http://www.uniprot.org/uniprot/P29965         http://www.ncbi.nlm.nih.gov/pubmed/2072720011   3   2                       ...
RDF11   3   2         56
Resource Description                 Framework11   3   2                          57
Subject-Predicate-Object11   3   2                              58
11   3   2   59
11   3   2   60
OWL11   3   2         61
11   3   2   62
SPARQL11   3   2            63
11   3   2   64
RDF11   3   2         65
RSS11   3   2         66
11   3   2   67
→11   3   2       68
UniProt11   3   2             69
2007                                   RDF             http://dev.isb-sib.ch/projects/uniprot-rdf/11   3   2              ...
• UniProt             •             •             •→11   3   2               71
• RDF             •             • RDF11   3   2           72
http://dev.isb-sib.ch/projects/uniprot-rdf/intro.html11   3   2                                                           73
11   3   2   74
OWL             http://dev.isb-sib.ch/projects/uniprot-rdf/owl/11   3   2                                                 ...
11   3   2   76
11   3   2   77
11   3   2   78
Protein                          citation   Citation             Annotation11   3   2                                     ...
11   3   2   80
11   3   2   81
XML     RDF/XML             2.7GB   6.0GB    7.7GB             0.5GB   0.6GB    0.7GB11   3   2                           ...
DDBJ               RDF11   3   2           83
• DDBJ             •                      unirprot             •11   3   2                       84
PDBj   RDF11   3   2                85
• PDBj             •             •                 RDF             • PDBj XML   RDF/XML11   3   2                         ...
RDF              DDBJ       299    300GB   6.6G               PDBj     65378   133GB   1.4G             MEDLINE     617   ...
RDF11   3   2         88
LInked Life Data11   3   2                      89
http://linkedlifedata.com/about11   3   2                                     90
RDF             CSV             JSON             XML             RDF11   3   2                91
11   3   2   92
BBC                            Webhttp://www.bbc.co.uk/blogs/bbcinternet/2010/07/   bbc_world_cup_2010_dynamic_sem.html11 ...
11   3   2   94
11   3   2   95
11   3   2   96
URI   URI11   3   2               97
Linked Data11   3   2                 98
“Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”11   3   2                 ...
11   3   2   100
RDF11   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/     ...
• Google Refine   • Protégé             • Virtuoso       • Freebase.org             • 4store         • TogoWS REST API     ...
RDF             • Semantic-Systems-Biology.org             • Bio2RDF             • NeuroCommons             • Linked Life ...
http://www.oreilly.co.jp/books/9784873114521/11   3   2                                                   111
11   3   2   112
•             • 2003   NSF11   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
Bioconductor11   3   2                  122
Galaxy11   3   2            123
Cytoscape11   3   2               124
BioMart11   3   2             125
11   3   2   126
11   3   2   127
11   3   2   128
↑             ↓11   3   2       129
Galaxy11   3   2            130
http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter11   3   2                                                        131
11   3   2   132
Devil in the details,             Nature 470, 305-6, 17 Feb. 2011                     doi:10.1038/470305b     http://www.n...
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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
http://togodb.dbcls.jp/TBA/

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データ統合とサイバーインフラストラクチャ

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

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