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Mining molecules from text and data

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Lars Juhl Jensen
Lars Juhl Jensen
TechnologyEducation
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Mining molecules from text and data Lars Juhl Jensen
Reflect
augmented browsing
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009 O’Donoghue et al., Journal of Web Semantics , 2010
web services
 
STITCH
Kuhn et al., Nucleic Acids Research , 2010
>74,000 small molecules
>2.5 million proteins
630 genomes
Gleevec
 
evidence types
primary experimental data
physical interactions
 
curated knowledge
drug targets
pathways
>10 km
literature mining
co-mentioning
 
NLP Natural Language Processing
 
integration
incomparable data
quality scores
calibrate vs. gold standard
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
larsjuhljensen

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Mining molecules from text and data

Editor's Notes

  1. This is a conservative estimate based only on what is in PubMed Too much to read! Text mining used to extract relations Similar methods used to mine medical records and link diseases