Integration of heterogeneous data

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Lars Juhl Jensen

10th Course in Bioinformatics and Systems Biology for Molecular Biologists, Schloss Hohenkammer, Hohenkammer, Germany, March 15, 2010.

Integration of heterogeneous data Lars Juhl Jensen

data mining

text mining

interaction networks

Kuhn et al., Nucleic Acids Research , 2010

parts lists

630 genomes

2.5 million proteins

~74,000 small molecules

many databases

different formats

model organism databases

Ensembl

RefSeq

PubChem

genomic context

gene fusion

Korbel et al., Nature Biotechnology , 2004

conserved neighborhood

operons

Korbel et al., Nature Biotechnology , 2004

bidirectional promoters

Korbel et al., Nature Biotechnology , 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology , 2004

experimental data

gene coexpression

protein interactions

Jensen & Bork, Science , 2008

genetic interactions

Beyer et al., Nature Reviews Genetics , 2007

small molecule interactions

in vitro binding assays

cellular activity assays

many databases

GEO Gene Expression Omnibus

BIND Biomolecular Interaction Network Database

BioGRID General Repository for Interaction Datasets

DIP Database of Interacting Proteins

IntAct

MINT Molecular Interactions Database

HPRD Human Protein Reference Database

PDB Protein Data Bank

BindingDB

CTD Comparative Toxicogenomics Database

DrugBank

GLIDA GPCR-Ligand Database

MATADOR

PDSP K i Psycoactive Drug Screening Program

PharmGKB Pharmacogenomics Knowledge Base

different formats

different identifiers

partially redundant

Campillos & Kuhn et al., Science , 2008

curated knowledge

complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences , 2008

many databases

Gene Ontology

MIPS Munich Information center for Protein Sequences

KEGG Kyoto Encyclopedia of Genes and Genomes

MetaCyc

Reactome

PID NCI-Nature Pathway Interaction Database

high confidence

different formats

different identifiers

partially redundant

literature mining

>10 km

human readable

not computer readable

different names

text corpus

M EDLINE

SGD Saccharomyces Genome Database

The Interactive Fly

OMIM Online Mendelian Inheritance in Man

thesaurus

co-mentioning

statistical methods

NLP Natural Language Processing

[object Object],[object Object],[object Object],[object Object],[object Object]

restricted access

Reflect

augmented browsing

Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009

integration

the easy problems

many databases

different formats

different identifiers

partially redundant

parsers

thesaurus

book keeping

the hard problems

many data types

not comparable

variable quality

raw quality scores

intergenic distances

Korbel et al., Nature Biotechnology , 2004

correlations

reproducibility

von Mering et al., Nucleic Acids Research , 2005

score calibration

gold standard

von Mering et al., Nucleic Acids Research , 2005

spread over 630 genomes

transfer by orthology

von Mering et al., Nucleic Acids Research , 2005

two modes

COG mode

von Mering et al., Nucleic Acids Research , 2005

protein mode

von Mering et al., Nucleic Acids Research , 2005

combine all evidence

P = 1-(1-P 1 )(1-P 2 )(1-P 3 ) …

visualize

Kuhn et al., Nucleic Acids Research , 2010

access

access for humans

web interfaces

access for computers

web services

REST Representational State Transfer

SOAP Simple Object Access Protocol

Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Integration of heterogeneous data

1. Integration of heterogeneous data Lars Juhl Jensen

2.

3.

4.

5.

8. interaction networks

9.

10. Kuhn et al., Nucleic Acids Research , 2010

11. parts lists

12. 630 genomes

13. 2.5 million proteins

14. ~74,000 small molecules

15. many databases

16. different formats

17. model organism databases

21. genomic context

22. gene fusion

23. Korbel et al., Nature Biotechnology , 2004

24. conserved neighborhood

26. Korbel et al., Nature Biotechnology , 2004

27. bidirectional promoters

28. Korbel et al., Nature Biotechnology , 2004

29. phylogenetic profiles

30. Korbel et al., Nature Biotechnology , 2004

31. experimental data

32. gene coexpression

33.

34. protein interactions

35. Jensen & Bork, Science , 2008

36. genetic interactions

37. Beyer et al., Nature Reviews Genetics , 2007

38. small molecule interactions

39. in vitro binding assays

40. cellular activity assays

41. many databases

42. GEO Gene Expression Omnibus

43. BIND Biomolecular Interaction Network Database

44. BioGRID General Repository for Interaction Datasets

45. DIP Database of Interacting Proteins

47. MINT Molecular Interactions Database

48. HPRD Human Protein Reference Database

49. PDB Protein Data Bank

51. CTD Comparative Toxicogenomics Database

53. GLIDA GPCR-Ligand Database

55. PDSP K i Psycoactive Drug Screening Program

56. PharmGKB Pharmacogenomics Knowledge Base

57. different formats

58. different identifiers

59. partially redundant

60. Campillos & Kuhn et al., Science , 2008

61. curated knowledge

64. Letunic & Bork, Trends in Biochemical Sciences , 2008

65. many databases

66. Gene Ontology

67. MIPS Munich Information center for Protein Sequences

68. KEGG Kyoto Encyclopedia of Genes and Genomes

71. PID NCI-Nature Pathway Interaction Database

72. high confidence

73. different formats

74. different identifiers

75. partially redundant

76. literature mining

78. human readable

79. not computer readable

80. different names

81. text corpus

83. SGD Saccharomyces Genome Database

84. The Interactive Fly

85. OMIM Online Mendelian Inheritance in Man

87. co-mentioning

88. statistical methods

89. NLP Natural Language Processing

90.

91.

92. restricted access

94. augmented browsing

95. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009

96. integration

97. the easy problems

98. many databases

99. different formats

100. different identifiers

101. partially redundant

104. book keeping

105. the hard problems

106. many data types

107. not comparable

108. variable quality

109. raw quality scores

110. intergenic distances

111. Korbel et al., Nature Biotechnology , 2004

112. correlations

113.

114. reproducibility

115. von Mering et al., Nucleic Acids Research , 2005

116. score calibration

117. gold standard

118. von Mering et al., Nucleic Acids Research , 2005

119. spread over 630 genomes

120. transfer by orthology

121. von Mering et al., Nucleic Acids Research , 2005

124. von Mering et al., Nucleic Acids Research , 2005

125. protein mode

126. von Mering et al., Nucleic Acids Research , 2005

127. combine all evidence

128. P = 1-(1-P 1 )(1-P 2 )(1-P 3 ) …

130. Kuhn et al., Nucleic Acids Research , 2010

132. access for humans

133. web interfaces

134.

135.

136.

137. access for computers

138. web services

139. REST Representational State Transfer

140. SOAP Simple Object Access Protocol

141.

142. larsjuhljensen