14th International Conference on Intelligent Systems for Molecular Biology, Tutorial, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006

1. Biological literature mining from information retrieval to biological discovery Lars Juhl Jensen EMBL, Germany [email_address]

2. Why do we need it?

6. Information Retrieval and Entity Recognition Lars Juhl Jensen EMBL, Germany [email_address]

29. Information Extraction and Text/Data Mining Lars Juhl Jensen , EMBL, Germany [email_address]

40. [ 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_activation_passive [ expression IL-13 expression ] induced by IL-2 + IL-18 ] [ expression_repression_active IL-10 also decreased [ expression mRNA expression of IL-2 and IL-18 cytokine receptors ] [ expression_repression_active Btk regulates the IL-2 gene ]

46. Time

47. Successful genes

48. Buzzwords

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

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

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

60. G2D

68. Outlook Lars Juhl Jensen EMBL, Germany [email_address]