Literature mining: what is it, and should I care?
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Literature mining
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EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 10, 2008
Transcript of Literature mining: what is it, and should I care?
Literature mining
Explosion
exponential increase
some things never change
“graph calculus”
=
~50 seconds per paper
Information retrieval
find the relevant papers
ad hoc retrieval
user-specified query
“yeast AND cell cycle”
stemming
yeast / yeasts
dynamic query expansion
yeast / S. cerevisiae
ranking
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
no tool will find it
Entity recognition
identify the substance(s)
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
good synonyms list
orthographic variation
CDC28
Cdc28p
disambiguation
Cdc2
APC
still too much to read
Information extraction
formalize the facts
co-mentioning
NLPNatural Language Processing
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
database
integration
STRING & STITCH
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
