2nd European Conference on Scientific Publishing in Biomedicine and Medicine, Rikshospitalet, Oslo, Norway, September 5-6, 2008

1. Integration of biomedical literature and databases Lars Juhl Jensen EMBL Heidelberg

2. biomedical databases

3. DNA sequences

4. GenBank

6. protein sequences

7. UniProt

9. protein structures

10. PDB

12. expression

13. ArrayExpress

14. GEO Gene Expression Omnibus

16. modifications

17. Phospho.ELM

18. PhosphoSite

19. interactions

20. BioGRID

21. DIP Database of Interacting Proteins

22. IntAct

23. MINT Molecular Interactions Database

25. chemical compounds

26. PubChem

28. database of databases

29. Duncan Hull, nodalpoint.org

30. freely available

31. literature mining

32. PubMed

33. exponential increase

36. some things never change

38. “ graph calculus”

39. =

40. ~50 seconds per paper

41. information retrieval

42. find the relevant papers

43. ad hoc retrieval

44. user-specified query

45. “ yeast AND cell cycle”

46. stemming

47. yeast / yeasts

48. dynamic query expansion

49. yeast / S. cerevisiae

54. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation

55. no tool will find it

56. entity recognition

57. identify the substance(s)

58. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation

59. good synonyms list

60. orthographic variation

61. CDC28

62. Cdc28p

63. disambiguation

64. Cdc2

65. SDS

66. information extraction

67. formalize the facts

68. co-mentioning

69. NLP Natural Language Processing

70. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation

71. integration tools

72. “ document-centric” tools

73. Reflect

75. browser add-on

76. real-time tagging service

77. any HTML document

78. augmented document

79. information from databases

81. iHOP

83. web interface

84. precomputed index

85. abstracts

86. find text about a protein

87. link proteins and text

89. experimental interactions

91. “ entity-centric” tools

92. STRING & STITCH

95. functional associations

96. heterogeneous evidence

97. information extraction

99. curated knowledge

101. interaction data

103. expression data

105. genomic context

107. quality scores

108. probabilistic framework

109. cross-species transfer

110. association networks

114. hands-on exercises