The document discusses the STRING database, which integrates various biological data sources to analyze functional interactions across 179 proteomes. It highlights methods for gene and protein interactions, including benchmarking against existing data and literature mining techniques. Acknowledgments are given to the STRING team and contributors for their work on the database and methodologies used.

1. The STRING database Lars Juhl Jensen EMBL Heidelberg

2. data integration

4. functional interactions

6. 179 proteomes

7. Ensembl

8. SWISS-PROT

9. genomic context methods

10. phylogenetic profiles

15. Cell Cellulosomes Cellulose

16. gene fusion

18. gene neighborhood

20. questionable reliability

21. raw quality scores

22. gene neighborhood

23. sum of intergenic distances

25. many types of evidence

26. raw quality scores

27. not directly comparable

28. benchmarking

29. calibrate against KEGG

31. curated knowledge

32. KEGG Kyoto Encyclopedia of Genes and Genomes

33. Reactome

34. MIPS Munich Information center for Protein Sequences

35. STKE Signal Transduction Knowledge Environment

36. primary experimental data

37. many sources

38. parsers

39. co-expression

40. GEO Gene Expression Omnibus

41. SMD Stanford Microarray Database

42. physical protein interactions

43. BIND Biomolecular Interaction Network Database

44. MINT Molecular Interactions Database

45. GRID General Repository for Interaction Datasets

46. DIP Database of Interacting Proteins

47. HPRD Human Protein Reference Database

48. literature mining

49. different gene identifiers

50. synonyms lists

51. M EDLINE

52. SGD Saccharomyces Genome Database

53. The Interactive Fly

54. OMIM Online Mendelian Inheritance in Man

55. co-mentioning

56. NLP Natural Language Processing

57. Gene and protein names Cue words for entity recognition Verbs for relation extraction [ nxgene The GAL4 gene ] [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]

59. combine all evidence

60. spread over many species

61. transfer by orthology

63. orthologous groups

65. fuzzy orthology

66. ? Source species Target species

67. Bayesian scoring scheme

69. Acknowledgments The STRING team (EMBL) Christian von Mering Berend Snel Martijn Huynen Sean Hooper Samuel Chaffron Julien Lagarde Mathilde Foglierini Peer Bork Literature mining project (EML Research) Jasmin Saric Rossitza Ouzounova Isabel Rojas