The STITCH and Reflect web resources

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Lars Juhl Jensen

Workshop on Drug Discovery Informatics, Technical University of Denmark, Lyngby, Denmark, January 26, 2010.

The STITCH and Reflect web resources Lars Juhl Jensen

STITCH

Kuhn et al., Nucleic Acids Research , 2010

REST web service

bulk download

parts lists

630 genomes

>2.5 million proteins

many databases

different formats

model organism databases

Ensembl

RefSeq

PubChem compounds

>74,000 small molecules

curated knowledge

complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences , 2008

high confidence

many databases

MIPS Munich Information center for Protein Sequences

Gene Ontology

KEGG Kyoto Encyclopedia of Genes and Genomes

MetaCyc

PID NCI-Nature Pathway Interaction Database

Reactome

different formats

different identifiers

partially redundant

interaction data

protein–small molecule

in vitro binding assays

protein–protein

yeast two-hybrid

affinity purification

fragment complementation

Jensen & Bork, Science , 2008

genetic interactions

Beyer et al., Nature Reviews Genetics , 2007

gene coexpression

many databases

BindingDB

CTD Comparative Toxicogenomics Database

DrugBank

GLIDA GPCR-Ligand Database

PDSP K i Psycoactive Drug Screening Program

PharmGKB Pharmacogenomics Knowledge Base

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

GEO Gene Expression Omnibus

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

dictionary

co-mentioning

NLP Natural Language Processing

restricted access

Reflect

augmented browsing

browser add-on

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

web interface

REST web service

SOAP web service

collaborate publishers

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

integration

many data types

not comparable

variable quality

spread over 630 genomes

quality scores

calibrate vs. gold standard

von Mering et al., Nucleic Acids Research , 2005

probabilistic scores

orthology transfer

von Mering et al., Nucleic Acids Research , 2005

combine all evidence

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1. The STITCH and Reflect web resources Lars Juhl Jensen

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

4. REST web service

5. bulk download

8. >2.5 million proteins

9. many databases

10. different formats

11. model organism databases

14. PubChem compounds

15. >74,000 small molecules

16. curated knowledge

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

20. high confidence

21. many databases

22. MIPS Munich Information center for Protein Sequences

23. Gene Ontology

24. KEGG Kyoto Encyclopedia of Genes and Genomes

26. PID NCI-Nature Pathway Interaction Database

28. different formats

29. different identifiers

30. partially redundant

31. interaction data

32. protein–small molecule

33. in vitro binding assays

34. protein–protein

35. yeast two-hybrid

36. affinity purification

37. fragment complementation

38. Jensen & Bork, Science , 2008

39. genetic interactions

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

41. gene coexpression

42.

43. many databases

45. CTD Comparative Toxicogenomics Database

47. GLIDA GPCR-Ligand Database

48. PDSP K i Psycoactive Drug Screening Program

49. PharmGKB Pharmacogenomics Knowledge Base

50. BIND Biomolecular Interaction Network Database

51. BioGRID General Repository for Interaction Datasets

52. DIP Database of Interacting Proteins

54. MINT Molecular Interactions Database

55. HPRD Human Protein Reference Database

56. PDB Protein Data Bank

57. GEO Gene Expression Omnibus

58. different formats

59. different identifiers

60. partially redundant

61. literature mining

63. human readable

64. not computer readable

65. different names

66. text corpus

68. SGD Saccharomyces Genome Database

69. The Interactive Fly

70. OMIM Online Mendelian Inheritance in Man

72. co-mentioning

73. NLP Natural Language Processing

74.

75. restricted access

77. augmented browsing

78. browser add-on

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

80. web interface

81.

82. REST web service

83. SOAP web service

84. collaborate publishers

85.

86. genomic context

87. gene fusion

88. Korbel et al., Nature Biotechnology , 2004

89. conserved neighborhood

91. Korbel et al., Nature Biotechnology , 2004

92. bidirectional promoters

93. Korbel et al., Nature Biotechnology , 2004

94. phylogenetic profiles

95. Korbel et al., Nature Biotechnology , 2004

96. integration

97. many data types

98. not comparable

99. variable quality

100. spread over 630 genomes

101. quality scores

102. calibrate vs. gold standard

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

104. probabilistic scores

105. orthology transfer

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

107. combine all evidence

108.

109.

110. larsjuhljensen

Notas do Editor

This is a conservative estimate based only on what is in PubMed Too much to read! Text mining used to extract relations Similar methods used to mine medical records and link diseases