Large-scale integration of data and text

Lars Juhl Jensen

cellular network biology

association networks

guilt by association

molecular networks

proteins

string-db.org

small molecules

stitch-db.org

subcellular localization

compartments.jensenlab.org

tissue expression

tissues.jensenlab.org

disease associations

usage statistics

heavily used

especially in the US

data integration

heterogeneous data

curated knowledge

experimental data

computational predictions

many databases

different formats

different identifiers

variable quality

not comparable

hard work

common identifiers

quality scores

score calibration

missing most of the data

text mining

>10 km

named entity recognition

comprehensive lexicon

cyclin dependent kinase 1

CDC2

orthographic variation

hCdc2

“black list”

SDS

co-mentioning

counting

within documents

within paragraphs

within sentences

IDG-specific tasks

target classification

text mining

“protein studiedness”

probabilistic counting

resource integration

disease associations

tissue expression

subcellular localization

automation of updates

web services

remapping of identifiers

predictions for dark matter

network-based inference

questions?