reflect and friends - tools and resources for mining biomedical text
TRANSCRIPT
Lars Juhl Jensen
Reflect and friendsTools and resources for mining biomedical text
>10 km
exponential growth
some things are constant
~45 seconds per paper
computer
as smart as a dog
teach it specific tricks
named 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
conflict resolution
“black list”
scalable implementation
>10 km<10 hours
augmented browsing
Reflect
reflect.ws
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
browser add-on
Firefox
Google Chrome
Safari
Internet Explorer
PDF viewer
Utopia Documents
collaborate with publishers
SciVerse application
corpora
~20 mio. abstracts
1.8 mio. full-text articles
collaborate with publishers
web-centric databases
guilt by association
information extraction
co-mentioning
STRING
string-db.org
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
~2.6 million proteins
STITCH
stitch-db.org
Kuhn et al., Nucleic Acids Research, 2012
~300,000 small molecules
COMPARTMENTS
subcellular localization
compartments.jensenlab.org
search for proteins
DISEASES
>8,000 disease terms
diseases.jensenlab.org
search for diseases
search for proteins
evidence viewers
disease behavior
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