The STITCH and Reflect web resources

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Workshop on Drug Discovery Informatics, Technical University of Denmark, Lyngby, Denmark, January 26, 2010.

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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. curated knowledge
    17. 17. complexes
    18. 18. pathways
    19. 19. Letunic & Bork, Trends in Biochemical Sciences , 2008
    20. 20. high confidence
    21. 21. many databases
    22. 22. MIPS Munich Information center for Protein Sequences
    23. 23. Gene Ontology
    24. 24. KEGG Kyoto Encyclopedia of Genes and Genomes
    25. 25. MetaCyc
    26. 26. PID NCI-Nature Pathway Interaction Database
    27. 27. Reactome
    28. 28. different formats
    29. 29. different identifiers
    30. 30. partially redundant
    31. 31. interaction data
    32. 32. protein–small molecule
    33. 33. in vitro binding assays
    34. 34. protein–protein
    35. 35. yeast two-hybrid
    36. 36. affinity purification
    37. 37. fragment complementation
    38. 38. Jensen & Bork, Science , 2008
    39. 39. genetic interactions
    40. 40. Beyer et al., Nature Reviews Genetics , 2007
    41. 41. gene coexpression
    42. 43. many databases
    43. 44. BindingDB
    44. 45. CTD Comparative Toxicogenomics Database
    45. 46. DrugBank
    46. 47. GLIDA GPCR-Ligand Database
    47. 48. PDSP K i Psycoactive Drug Screening Program
    48. 49. PharmGKB Pharmacogenomics Knowledge Base
    49. 50. BIND Biomolecular Interaction Network Database
    50. 51. BioGRID General Repository for Interaction Datasets
    51. 52. DIP Database of Interacting Proteins
    52. 53. IntAct
    53. 54. MINT Molecular Interactions Database
    54. 55. HPRD Human Protein Reference Database
    55. 56. PDB Protein Data Bank
    56. 57. GEO Gene Expression Omnibus
    57. 58. different formats
    58. 59. different identifiers
    59. 60. partially redundant
    60. 61. literature mining
    61. 62. >10 km
    62. 63. human readable
    63. 64. not computer readable
    64. 65. different names
    65. 66. text corpus
    66. 67. M EDLINE
    67. 68. SGD Saccharomyces Genome Database
    68. 69. The Interactive Fly
    69. 70. OMIM Online Mendelian Inheritance in Man
    70. 71. dictionary
    71. 72. co-mentioning
    72. 73. NLP Natural Language Processing
    73. 75. restricted access
    74. 76. Reflect
    75. 77. augmented browsing
    76. 78. browser add-on
    77. 79. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    78. 80. web interface
    79. 82. REST web service
    80. 83. SOAP web service
    81. 84. collaborate publishers
    82. 86. genomic context
    83. 87. gene fusion
    84. 88. Korbel et al., Nature Biotechnology , 2004
    85. 89. conserved neighborhood
    86. 90. operons
    87. 91. Korbel et al., Nature Biotechnology , 2004
    88. 92. bidirectional promoters
    89. 93. Korbel et al., Nature Biotechnology , 2004
    90. 94. phylogenetic profiles
    91. 95. Korbel et al., Nature Biotechnology , 2004
    92. 96. integration
    93. 97. many data types
    94. 98. not comparable
    95. 99. variable quality
    96. 100. spread over 630 genomes
    97. 101. quality scores
    98. 102. calibrate vs. gold standard
    99. 103. von Mering et al., Nucleic Acids Research , 2005
    100. 104. probabilistic scores
    101. 105. orthology transfer
    102. 106. von Mering et al., Nucleic Acids Research , 2005
    103. 107. combine all evidence
    104. 109. 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>Heiko Horn </li></ul></ul><ul><ul><li>Sune Frankild </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Nigel Brown </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>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>
    105. 110. larsjuhljensen

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