The STITCH and Reflect web resources

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Lars Juhl Jensen

The document discusses two web resources called STITCH and Reflect that integrate biological data from multiple sources. STITCH provides a REST web service for bulk downloading parts lists and protein information from 630 genomes and databases in different formats. Reflect provides augmented browsing of biological data through a browser add-on and allows collaboration. It integrates multiple data types from sources with variable quality that are spread across 630 genomes.

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

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

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

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

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.ws

augmented browsing

browser add-on

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

Firefox

Internet Explorer

Google Chrome

Utopia

PDF viewer

web services

collaborate industry

intranet solution

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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larsjuhljensen

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The STITCH and Reflect web resources

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. genomic context

17. gene fusion

18. Korbel et al., Nature Biotechnology , 2004

19. conserved neighborhood

21. Korbel et al., Nature Biotechnology , 2004

22. bidirectional promoters

23. Korbel et al., Nature Biotechnology , 2004

24. phylogenetic profiles

25. Korbel et al., Nature Biotechnology , 2004

26. interaction data

27. protein–small molecule

28. in vitro binding assays

29. protein–protein

30. yeast two-hybrid

31. affinity purification

32. fragment complementation

33. Jensen & Bork, Science , 2008

34. genetic interactions

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

36. gene coexpression

37.

38. many databases

40. CTD Comparative Toxicogenomics Database

42. GLIDA GPCR-Ligand Database

43. PDSP K i Psycoactive Drug Screening Program

44. PharmGKB Pharmacogenomics Knowledge Base

45. BIND Biomolecular Interaction Network Database

46. BioGRID General Repository for Interaction Datasets

47. DIP Database of Interacting Proteins

49. MINT Molecular Interactions Database

50. HPRD Human Protein Reference Database

51. PDB Protein Data Bank

52. GEO Gene Expression Omnibus

53. different formats

54. different identifiers

55. partially redundant

56. curated knowledge

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

60. high confidence

61. many databases

62. MIPS Munich Information center for Protein Sequences

63. Gene Ontology

64. KEGG Kyoto Encyclopedia of Genes and Genomes

66. PID NCI-Nature Pathway Interaction Database

68. different formats

69. different identifiers

70. partially redundant

71. literature mining

73. human readable

74. not computer readable

75. different names

76. text corpus

78. SGD Saccharomyces Genome Database

79. The Interactive Fly

80. OMIM Online Mendelian Inheritance in Man

82. co-mentioning

83. NLP Natural Language Processing

84.

85. restricted access

87. augmented browsing

88.

89. browser add-on

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

92. Internet Explorer

93. Google Chrome

96. web services

97. collaborate industry

98.

99.

100. intranet solution

101. integration

102. many data types

103. not comparable

104. variable quality

105. spread over 630 genomes

106. quality scores

107. calibrate vs. gold standard

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

109. probabilistic scores

110. orthology transfer

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

112. combine all evidence

113.

114.

115. larsjuhljensen

Notas del 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