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Turning literature into databases

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Lars Juhl Jensen
Lars Juhl Jensen
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Turning literature into databases >10 km Lars Juhl Jensen
corpora
22M abstracts
1.9M freely available articles
1.9M Elsevier documents
entity recognition
identify the concepts
comprehensive lexicon
small molecules
proteins
cellular components
tissues
organisms
phenotypes
diseases
orthographic variation
singular vs. plural
flexible matching
spaces and hyphens
“black list”
information extraction
count co-mentioning
within documents
within paragraphs
within sentences
new scoring scheme
STRING v9.1
~2x better sensitivity
web-centric databases
suite of web interfaces
common backend database
diseases.jensenlab.org
search for a protein
ranked table of diseases
search for a disease
STRING network
evidence viewer
compartments.jensenlab.org
text mining
curated knowledge
sequence-based predictions
visualization
tissues.jensenlab.org
related projects
importance of full text
NIH grant abstracts
electronic patient records
patient stratification
Roque et al., PLoS Computational Biology, 2011
pharmacovigilance
Eriksson et al., in preparation, 2012
Thank you! Sune Frankild Janos Binder Kalliopi Tsafou Peter Bjødstrup Jensen Robert Eriksson
Turning literature into databases

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Turning literature into databases