The STRING database
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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.
![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/jen06talk9-1217971178211118-9/85/The-STRING-database-57-320.jpg)
The STRING database
- 1. The STRING database Lars Juhl Jensen EMBL Heidelberg
- 7. Ensembl
- 8. SWISS-PROT
- 16. gene fusion
- 23. sum of intergenic distances
- 25. many types of evidence
- 28. benchmarking
- 32. KEGG Kyoto Encyclopedia of Genes and Genomes
- 33. Reactome
- 34. MIPS Munich Information center for Protein Sequences
- 35. STKE Signal Transduction Knowledge Environment
- 37. many sources
- 38. parsers
- 39. co-expression
- 40. GEO Gene Expression Omnibus
- 41. SMD Stanford Microarray Database
- 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
- 50. synonyms lists
- 51. M EDLINE
- 52. SGD Saccharomyces Genome Database
- 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 ]
- 60. spread over many species
- 65. fuzzy orthology
- 66. ? Source species Target species
- 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