BioSys course, Technical University of Denmark, Lyngby, Denmark, October 24, 2005

1. Biological Literature Mining Lars Juhl Jensen EMBL

2. Why?

8. Information Retrieval and Text Categorization Lars Juhl Jensen EMBL

26. Entity Recognition and Information Extraction Lars Juhl Jensen EMBL

47. [ expression_repression_active Btk regulates the IL-2 gene ] [ dephosphorylation_nominal Dephosphorylation of Syk and Btk mediated by SHP-1 ] [ phosphorylation_nominal phosphorylation of Shc by the hematopoietic cell-specific tyrosine kinase Syk ] [ phosphorylation_nominal the phosphorylation of the adapter protein SHC by the Src-related kinase Lyn ] [ phosphorylation_active Lyn also participates in [ phosphorylation the tyrosine phosphorylation and activation of syk ]] [ phosphorylation_active Lyn , [ negation but not Jak2 ] phosphorylated CrkL ] [ phosphorylation_active Lyn , [ negation but not Jak2 ] phosphorylated CrkL ] [ phosphorylation_active Lyn also participates in [ phosphorylation the tyrosine phosphorylation and activation of syk ]] [ phosphorylation_nominal the phosphorylation of the adapter protein SHC by the Src-related kinase Lyn ] [ phosphorylation_nominal phosphorylation of Shc by the hematopoietic cell-specific tyrosine kinase Syk ] [ dephosphorylation_nominal Dephosphorylation of Syk and Btk mediated by SHP-1 ] [ expression_repression_active IL-10 also decreased [ expression mRNA expression of IL-2 and IL18 cytokine receptors] [ expression_repression_active IL-10 also decreased [ expression mRNA expression of IL-2 and IL18 cytokine receptors ] [ expression_activation_passive [ expression IL-13 expression] induced by IL-2 + IL-18 ] [ expression_activation_passive [ expression IL-13 expression ] induced by IL-2 + IL-18 ] [ expression_repression_active Btk regulates the IL-2 gene ]

49. MedScan

51. Text- and Data-mining Lars Juhl Jensen EMBL

54. Time

55. Successful genes

56. Buzzwords

58. Transcriptional networks 32 79 83 3592 Regulates Regulated P < 9  10 -9

59. Signaling pathways 11 27 44 3704 Phosphorylates Phosphorylated P < 2  10 -7

60. Multiple regulation 8 107 47 3625 Expression Phosphorylation P < 5  10 -4

71. RCCs

73. G2D

82. Outlook Lars Juhl Jensen EMBL

87. Exercises Lars Juhl Jensen EMBL