literature mining: what is it, and should i care?
DESCRIPTION
EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 10, 2008TRANSCRIPT
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Literature mining
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Explosion
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exponential increase
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some things never change
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“graph calculus”
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=
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~50 seconds per paper
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Information retrieval
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find the relevant papers
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ad hoc retrieval
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user-specified query
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“yeast AND cell cycle”
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stemming
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yeast / yeasts
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dynamic query expansion
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yeast / S. cerevisiae
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ranking
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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
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no tool will find it
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Entity recognition
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identify the substance(s)
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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
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good synonyms list
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orthographic variation
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CDC28
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Cdc28p
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disambiguation
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Cdc2
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APC
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still too much to read
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Information extraction
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formalize the facts
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co-mentioning
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NLPNatural Language Processing
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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
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database
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integration
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STRING & STITCH
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Acknowledgments
STRING & STITCH– Christian von Mering
– Michael Kuhn
– Manuel Stark
– Samuel Chaffron
– Philippe Julien
– Tobias Doerks
– Jan Korbel
– Berend Snel
– Martijn Huynen
– Peer Bork
The movie “Brazil”
Reflect– Evangelos Pafilis
– Michael Kuhn
– Heiko Horn
– Peer Bork
– Sean O’Donoghue
– Reinhardt Schneider
NLP pipeline– Jasmin Saric
– Rossitza Ouzounova
– Isabel Rojas
– Peer Bork