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Lars Juhl Jensen
Reflect and friendsTools and resources for mining biomedical text
>10 km
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exponential growth
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some things are constant
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~45 seconds per paper
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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identify the concepts
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comprehensive lexicon
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small molecules
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proteins
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cellular components
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tissues
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organisms
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phenotypes
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diseases
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orthographic variation
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singular vs. plural
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flexible matching
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spaces and hyphens
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conflict resolution
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“black list”
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scalable implementation
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>10 km<10 hours
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augmented browsing
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Reflect
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reflect.ws
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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browser add-on
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Firefox
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Google Chrome
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Safari
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Internet Explorer
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PDF viewer
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Utopia Documents
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collaborate with publishers
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SciVerse application
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corpora
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~20 mio. abstracts
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1.8 mio. full-text articles
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collaborate with publishers
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web-centric databases
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guilt by association
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information extraction
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co-mentioning
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STRING
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string-db.org
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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~2.6 million proteins
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STITCH
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stitch-db.org
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Kuhn et al., Nucleic Acids Research, 2012
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~300,000 small molecules
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COMPARTMENTS
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subcellular localization
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compartments.jensenlab.org
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search for proteins
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DISEASES
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>8,000 disease terms
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diseases.jensenlab.org
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search for diseases
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search for proteins
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evidence viewers
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disease behavior
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Thank you!
STRING and STITCH
Damian Szklarczyk
Andrea Franceschini
Michael Kuhn
Milan Simonovic
Alexander Roth
Pablo Minguez
Tobias Doerks
Manuel Stark
Jean Muller
Peer Bork
Christian von Mering
Reflect
Sune Frankild
Heiko Horn
Evangelos Pafilis
Janos Binder
Reinhardt Schneider
Sean O’Donoghue
COMPARTMENTSand DISEASES
Sune Frankild
Janos Binder