Lars Juhl Jensen

Text mining for organismand environment names

who am I?

sequence analysis

protein networks

string-db.org

chemical networks

stitch-db.org

group leader

proteomics

subcellular localization

compartments.jensenlab.org

tissue expression

tissues.jensenlab.org

disease associations

medical informatics

Jensen et al., Nature Reviews Genetics, 2012

cofounder

me

why text mining?

data mining

unstructured text

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

organisms

environments

expansion rules

plural and adjective forms

flexible matching

hyphens and spaces

“black list”

a

execution modes

C++ batch tagger

Python API

web service

questions?