Lars Juhl Jensen

The pragmatic text minerIt’s just another type of poorly standardized

data

why text mining?

data mining

guilt by association

structured data

unstructured text

biomedical literature

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

synonyms

prostate specific antigen

KLK3

expansion rules

prefixes and suffixes

KLK3

hKLK3

flexible matching

hyphens and spaces

prostate specific antigen

prostate-specific antigen

“black list”

SDS

co-mentioning

within documents

within paragraphs

within sentences

weighted score

text corpus

what we normally use

Medline abstracts

what we should use

full-text articles

many publishers

different interfaces

different formats

different licenses

unclear terms

unifying text & data

text mining

curated knowledge

experimental data

computational predictions

integrated web resources

protein networks

string-db.org

chemical networks

stitch-db.org

subcellular localization

compartments.jensenlab.org

tissue expression

tissues.jensenlab.org

disease associations

many sources

different formats

different identifiers

variable quality

not comparable

hard work

common identifiers

quality scores

score calibration

data visualization

collaboration model

domain experts

what?

why?

problem

manpower

me

how?

technology

guidance

biodiversity

organisms

environments

Encyclopedia of Life

Biodiversity Heritage Library

pharmacovigilance

drugs

adverse drug reactions

electronic health records

what we need

one place to get all

the format is not crucial

the license is

AcknowledgmentsProtein networks

Michael KuhnDamian Szklarczyk

Andrea Franceschini Milan SimonovicAlexander RothSune Pletscher-

FrankildJianyi Lin

Pablo MinguezChristian von Mering

Peer Bork

Localization and diseaseSune Pletscher-FrankildAlberto SantosJanos BinderKalliopi TsafouChristian StolteAlbert PallejaHeiko HornEvangelos PafilisReinhardt SchneiderSean O’ Donoghue