Text mining and data integration
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Text mining and data integration
- 1. Lars Juhl Jensen Text mining and data integration
- 5. ~45 seconds per paper
- 10. data integration
- 12. find the relevant papers
- 13. ad hoc retrieval
- 15. “yeast AND cell cycle”
- 16. PubMed
- 18. indexing
- 19. fast lookup
- 20. stemming
- 21. word endings
- 23. MeSH terms
- 24. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
- 25. no tool will find that
- 27. computer
- 28. as smart as a dog
- 29. teach it specific tricks
- 33. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
- 35. CDC2
- 36. cyclin dependent kinase 1
- 39. CDC2
- 40. Cdc2
- 42. cyclin dependent kinase 1
- 45. CDC2
- 46. hCDC2
- 47. “black list”
- 48. SDS
- 50. >10 km <10 hours
- 52. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
- 53. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
- 54. Reflect
- 55. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
- 58. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
- 59. two approaches
- 60. co-mentioning
- 61. counting
- 62. within documents
- 64. within sentences
- 70. semantic tagging
- 71. sentence parsing
- 72. Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
- 74. high precision
- 75. poor recall
- 76. text corpus
- 78. few use full-text articles
- 79. no access
- 80. PDF files
- 83. my corpus
- 89. STRING
- 90. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
- 92. gene fusion
- 93. Korbel et al., Nature Biotechnology, 2004
- 95. Korbel et al., Nature Biotechnology, 2004
- 97. Korbel et al., Nature Biotechnology, 2004
- 98. a real example
- 103. experimental data
- 104. gene coexpression
- 107. Jensen & Bork, Science, 2008
- 108. curated knowledge
- 109. pathways
- 110. Letunic & Bork, Trends in Biochemical Sciences, 2008
- 111. many databases
- 112. different formats
- 114. variable quality
- 115. not comparable
- 116. hard work
- 117. quality scores
- 118. von Mering et al., Nucleic Acids Research, 2005
- 119. calibrate vs. gold standard
- 120. von Mering et al., Nucleic Acids Research, 2005
- 121. data integration
- 122. general approach
- 123. suite of web resources
- 124. STITCH
- 125. STRING + 300k chemicals
- 126. Kuhn et al., Nucleic Acids Research, 2012
- 127. COMPARTMENTS
- 130. TISSUES
- 131. tissue expression
- 133. DISEASES
- 134. disease genes
- 135. unification
- 136. curated knowledge
- 137. text mining
- 138. experimental data
- 140. common identifiers
- 141. quality scores
- 142. visualization
- 143. dissemination
- 144. web interfaces
- 146. evidence viewers
- 148. web services
- 150. bulk download
- 151. thank you!