The STRING database
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The STRING database integrates known and predicted protein-protein interactions, including direct (physical) and indirect (functional) associations derived from genomic context, high-throughput experiments, co-expression and literature mining. It covers over 373 proteomes and draws on data from curated databases, textmining and computational prediction methods to provide a global network of protein interactions. STRING uses a scoring scheme to assign probabilities to interactions based on different lines of evidence and benchmarking against a gold standard reference set.
![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 ]](https://image.slidesharecdn.com/jen06talk15-1217973031154107-8/85/The-STRING-database-75-320.jpg)
The STRING database
- 1. The STRING database Lars Juhl Jensen EMBL Heidelberg
- 3. Jensen et al., Drug Discovery Today: Targets, 2004
- 5. Bork et al., Current Opinion in Structural Biology, 2005
- 8. RefSeq
- 9. Ensembl
- 12. gene fusion
- 22. automation
- 23. scoring scheme
- 26. gene fusion
- 30. sum of intergenic distances
- 33. SVD Singular Value Decomposition
- 37. not comparable
- 39. sum of intergenic distances
- 41. benchmarking
- 42. calibrate vs. gold standard
- 47. KEGG Kyoto Encyclopedia of Genes and Genomes
- 48. Reactome
- 49. MIPS Munich Information center for Protein Sequences
- 50. STKE Signal Transduction Knowledge Environment
- 52. many sources
- 53. many parsers
- 55. BIND Biomolecular Interaction Network Database
- 56. GRID General Repository for Interaction Datasets
- 57. MINT Molecular Interactions Database
- 58. DIP Database of Interacting Proteins
- 59. HPRD Human Protein Reference Database
- 60. merge data by publication
- 62. von Mering et al., Nucleic Acids Research, 2005
- 63. co-expression
- 64. GEO Gene Expression Omnibus
- 68. synonyms lists
- 69. M EDLINE
- 70. SGD Saccharomyces Genome Database
- 72. OMIM Online Mendelian Inheritance in Man
- 73. co-mentioning
- 74. NLP Natural Language Processing
- 75. 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 ]
- 76. calibrate vs. gold standard
- 79. spread over many species
- 81. von Mering et al., Nucleic Acids Research, 2005
- 82. two modes
- 85. von Mering et al., Nucleic Acids Research, 2005
- 86. fuzzy orthology
- 87. von Mering et al., Nucleic Acids Research, 2005
- 89. Bork et al., Current Opinion in Structural Biology, 2005
- 90. 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