The STITCH and Reflect web resources

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  • This is a conservative estimate based only on what is in PubMed Too much to read! Text mining used to extract relations Similar methods used to mine medical records and link diseases
  • The STITCH and Reflect web resources

    1. 1. The STITCH and Reflect web resources Lars Juhl Jensen
    2. 2. STITCH
    3. 3. Kuhn et al., Nucleic Acids Research , 2010
    4. 4. REST web service
    5. 5. bulk download
    6. 6. parts lists
    7. 7. 630 genomes
    8. 8. >2.5 million proteins
    9. 9. many databases
    10. 10. different formats
    11. 11. model organism databases
    12. 12. Ensembl
    13. 13. RefSeq
    14. 14. PubChem compounds
    15. 15. >74,000 small molecules
    16. 16. genomic context
    17. 17. gene fusion
    18. 18. Korbel et al., Nature Biotechnology , 2004
    19. 19. conserved neighborhood
    20. 20. operons
    21. 21. Korbel et al., Nature Biotechnology , 2004
    22. 22. bidirectional promoters
    23. 23. Korbel et al., Nature Biotechnology , 2004
    24. 24. phylogenetic profiles
    25. 25. Korbel et al., Nature Biotechnology , 2004
    26. 26. interaction data
    27. 27. protein–small molecule
    28. 28. in vitro binding assays
    29. 29. protein–protein
    30. 30. yeast two-hybrid
    31. 31. affinity purification
    32. 32. fragment complementation
    33. 33. Jensen & Bork, Science , 2008
    34. 34. genetic interactions
    35. 35. Beyer et al., Nature Reviews Genetics , 2007
    36. 36. gene coexpression
    37. 38. many databases
    38. 39. BindingDB
    39. 40. CTD Comparative Toxicogenomics Database
    40. 41. DrugBank
    41. 42. GLIDA GPCR-Ligand Database
    42. 43. PDSP K i Psycoactive Drug Screening Program
    43. 44. PharmGKB Pharmacogenomics Knowledge Base
    44. 45. BIND Biomolecular Interaction Network Database
    45. 46. BioGRID General Repository for Interaction Datasets
    46. 47. DIP Database of Interacting Proteins
    47. 48. IntAct
    48. 49. MINT Molecular Interactions Database
    49. 50. HPRD Human Protein Reference Database
    50. 51. PDB Protein Data Bank
    51. 52. GEO Gene Expression Omnibus
    52. 53. different formats
    53. 54. different identifiers
    54. 55. partially redundant
    55. 56. curated knowledge
    56. 57. complexes
    57. 58. pathways
    58. 59. Letunic & Bork, Trends in Biochemical Sciences , 2008
    59. 60. high confidence
    60. 61. many databases
    61. 62. MIPS Munich Information center for Protein Sequences
    62. 63. Gene Ontology
    63. 64. KEGG Kyoto Encyclopedia of Genes and Genomes
    64. 65. MetaCyc
    65. 66. PID NCI-Nature Pathway Interaction Database
    66. 67. Reactome
    67. 68. different formats
    68. 69. different identifiers
    69. 70. partially redundant
    70. 71. literature mining
    71. 72. >10 km
    72. 73. human readable
    73. 74. not computer readable
    74. 75. different names
    75. 76. text corpus
    76. 77. M EDLINE
    77. 78. SGD Saccharomyces Genome Database
    78. 79. The Interactive Fly
    79. 80. OMIM Online Mendelian Inheritance in Man
    80. 81. dictionary
    81. 82. co-mentioning
    82. 83. NLP Natural Language Processing
    83. 85. restricted access
    84. 86. Reflect.ws
    85. 87. augmented browsing
    86. 89. browser add-on
    87. 90. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    88. 91. Firefox
    89. 92. Internet Explorer
    90. 93. Google Chrome
    91. 94. Utopia
    92. 95. PDF viewer
    93. 96. web services
    94. 97. collaborate industry
    95. 100. intranet solution
    96. 101. integration
    97. 102. many data types
    98. 103. not comparable
    99. 104. variable quality
    100. 105. spread over 630 genomes
    101. 106. quality scores
    102. 107. calibrate vs. gold standard
    103. 108. von Mering et al., Nucleic Acids Research , 2005
    104. 109. probabilistic scores
    105. 110. orthology transfer
    106. 111. von Mering et al., Nucleic Acids Research , 2005
    107. 112. combine all evidence
    108. 114. Acknowledgments <ul><ul><li>STITCH </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Damian Szklarczyk </li></ul></ul><ul><ul><li>Andrea Franceschini </li></ul></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Lars Juhl Jensen </li></ul></ul><ul><ul><li>Andreas Beyer </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Reflect </li></ul></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Sune Frankild </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul><ul><ul><li>STRING </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Damian Szklarczyk </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Chris Creevey </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Alexander Roth </li></ul></ul><ul><ul><li>Milan Simonovic </li></ul></ul><ul><ul><li>Jan Korbel </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul>
    109. 115. larsjuhljensen
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