Bioinformatics & Gene Discovery, Technical University of Denmark, Lyngby, Denmark, January 2, 2006

1. Biological Literature Mining Lars Juhl Jensen EMBL

2. Why?

6. Information Retrieval and Entity Recognition Lars Juhl Jensen EMBL

30. Information Extraction and Text/Data Mining Lars Juhl Jensen EMBL

41. [ 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 ]

47. Time

48. Successful genes

49. Buzzwords

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

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

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

61. RCCs

63. G2D

72. Outlook Lars Juhl Jensen EMBL

77. Exercises Lars Juhl Jensen EMBL