Integration of heterogeneous data
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The document discusses the integration of heterogeneous biological data sources, including genomes, proteins, and small molecules, emphasizing their varying formats and identifiers. It highlights the challenges in data comparison and quality, as well as the importance of advanced methods in natural language processing for extracting relationships from literature. Various databases and methodologies for gene interactions, expression, and pathways are reviewed to enhance data accessibility for both humans and computational systems.
![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/jen10talk5-100315121007-phpapp02/85/Integration-of-heterogeneous-data-90-320.jpg)
Integration of heterogeneous data
- 1. Integration of heterogeneous data Lars Juhl Jensen
- 6. data mining
- 7. text mining
- 10. Kuhn et al., Nucleic Acids Research , 2010
- 11. parts lists
- 12. 630 genomes
- 15. many databases
- 18. Ensembl
- 19. RefSeq
- 20. PubChem
- 21. genomic context
- 22. gene fusion
- 23. Korbel et al., Nature Biotechnology , 2004
- 25. operons
- 26. Korbel et al., Nature Biotechnology , 2004
- 28. Korbel et al., Nature Biotechnology , 2004
- 30. Korbel et al., Nature Biotechnology , 2004
- 35. Jensen & Bork, Science , 2008
- 37. Beyer et al., Nature Reviews Genetics , 2007
- 39. in vitro binding assays
- 41. many databases
- 42. GEO Gene Expression Omnibus
- 43. BIND Biomolecular Interaction Network Database
- 44. BioGRID General Repository for Interaction Datasets
- 45. DIP Database of Interacting Proteins
- 46. IntAct
- 47. MINT Molecular Interactions Database
- 48. HPRD Human Protein Reference Database
- 49. PDB Protein Data Bank
- 50. BindingDB
- 51. CTD Comparative Toxicogenomics Database
- 52. DrugBank
- 54. MATADOR
- 55. PDSP K i Psycoactive Drug Screening Program
- 56. PharmGKB Pharmacogenomics Knowledge Base
- 60. Campillos & Kuhn et al., Science , 2008
- 62. complexes
- 63. pathways
- 64. Letunic & Bork, Trends in Biochemical Sciences , 2008
- 65. many databases
- 66. Gene Ontology
- 67. MIPS Munich Information center for Protein Sequences
- 68. KEGG Kyoto Encyclopedia of Genes and Genomes
- 69. MetaCyc
- 70. Reactome
- 71. PID NCI-Nature Pathway Interaction Database
- 72. high confidence
- 77. >10 km
- 78. human readable
- 80. different names
- 81. text corpus
- 82. M EDLINE
- 83. SGD Saccharomyces Genome Database
- 85. OMIM Online Mendelian Inheritance in Man
- 86. thesaurus
- 87. co-mentioning
- 89. NLP Natural Language Processing
- 90. 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 ]
- 93. Reflect
- 95. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
- 96. integration
- 98. many databases
- 101. partially redundant
- 102. parsers
- 103. thesaurus
- 104. book keeping
- 105. the hard problems
- 106. many data types
- 107. not comparable
- 108. variable quality
- 109. raw quality scores
- 110. intergenic distances
- 111. Korbel et al., Nature Biotechnology , 2004
- 112. correlations
- 114. reproducibility
- 115. von Mering et al., Nucleic Acids Research , 2005
- 116. score calibration
- 117. gold standard
- 118. von Mering et al., Nucleic Acids Research , 2005
- 119. spread over 630 genomes
- 121. von Mering et al., Nucleic Acids Research , 2005
- 122. two modes
- 123. COG mode
- 124. von Mering et al., Nucleic Acids Research , 2005
- 125. protein mode
- 126. von Mering et al., Nucleic Acids Research , 2005
- 127. combine all evidence
- 128. P = 1-(1-P 1 )(1-P 2 )(1-P 3 ) …
- 129. visualize
- 130. Kuhn et al., Nucleic Acids Research , 2010
- 131. access
- 132. access for humans
- 133. web interfaces
- 137. access for computers
- 138. web services
- 139. REST Representational State Transfer
- 140. SOAP Simple Object Access Protocol
- 141. Acknowledgments STITCH Michael Kuhn Damian Szklarczyk Andrea Franceschini Monica Campillos Christian von Mering Lars Juhl Jensen Andreas Beyer Peer Bork Reflect Sean O’Donoghue Heiko Horn Sune Frankild Evangelos Pafilis Michael Kuhn Nigel Brown Reinhardt Schneider STRING Christian von Mering Michael Kuhn Manuel Stark Samuel Chaffron Chris Creevey Jean Muller Tobias Doerks Philippe Julien Alexander Roth Milan Simonovic Jan Korbel Berend Snel Martijn Huynen Peer Bork
- 142. larsjuhljensen