one tagger, many uses: illustrating the power of dictionary-based named entity recognition

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Lars Juhl Jensen @larsjuhljensen One tagger, many uses Illustrating the power of dictionary-based named entity recognition

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Page 1: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Lars Juhl Jensen@larsjuhljensen

One tagger, many usesIllustrating the power of dictionary-based named entity

recognition

Page 2: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

>10 km

Page 3: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

too much to read

Page 4: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

computer

Page 5: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

as smart as a dog

Page 6: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

teach it specific tricks

Page 7: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Page 8: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Page 9: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

named entity recognition

Page 10: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

dictionary

Page 11: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

genes / proteins

Page 12: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

diseases

Page 13: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

expansion rules

Page 14: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

prefixes and suffixes

Page 15: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

curated blacklist

Page 16: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

SDS

Page 17: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

software

Page 18: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

C++ tagger

Page 19: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

>1000 abstracts / second

Page 20: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

70–80% recall

Page 21: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

80–90% precision

Page 22: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

open sourcebitbucket.org/larsjuhljensen/tagger/

Page 23: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Dockerhub.docker.com/r/larsjuhljensen/tagger/

Page 24: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

web servicetagger.jensenlab.org

Page 25: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

community resources

Page 26: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Extractextract.jensenlab.org

Page 27: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Page 28: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

STRINGstring-db.org

Page 29: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

string-db.org

Page 30: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

DISEASESdiseases.jensenlab.org

Page 31: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Cytoscape

Page 32: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Page 33: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

curated knowledge

Page 34: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

experimental data

Page 35: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

co-occurrence text mining

Page 36: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Medline abstracts

Page 37: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

<1 km

Page 38: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

15 million full-text articles

Page 39: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Westergaard et al., BioRxiv, 2017

Page 40: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

~50% more associations

Page 41: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

electronic health records

Page 42: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Jensen et al., Nature Reviews Genetics, 2012

Page 43: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Page 44: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

in Danish

Page 45: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

dictionary

Page 46: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

drugs

Page 47: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

adverse events

Page 48: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

in Danish

Page 49: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

named entity recognition

Page 50: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

temporal correlations

Page 51: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

Drug introduction Drug discontinuation

Adverse eventNegative modifier Indication Pre-existingcondition

Adverse drug reaction Possibleadverse drug reaction

Adverse event

ADR ofadditional drug

Identification start

Eriksson et al., Drug Safety, 2014

Page 52: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

find novel associations

Page 53: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

summary

Page 54: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

broadly applicable

Page 55: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

keep it simple

Page 56: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

free tools

Page 57: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

AcknowledgmentsEvangelos PafilisSune Pletscher-

FrankildNadezhda Doncheva

Damian SzklarczykMichael Kuhn

Robert Eriksson

John “Scooter” MorrisTudor OpreaChristian von MeringPeer BorkChristos ArvanitidisSøren Brunak

Page 58: One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

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