Lars Juhl Jensen

Mining literature and medical records

>10 km

exponential growth

~45 seconds per paper

outline

information retrieval

named entity recognition

augmented browsing

information extraction

text corpora

web resources

electronic health records

medical text mining

questions

information retrieval

find the relevant papers

ad hoc retrieval

user-specified query

“yeast AND cell cycle”

PubMed

indexing

fast lookup

stemming

word endings

dynamic query expansion

MeSH terms

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

no tool will find that

named entity recognition

identify the concepts

computer

as smart as a dog

teach it specific tricks

comprehensive lexicon

small molecules

proteins

cellular components

tissues

organisms

environments

diseases

phenotypes

behaviors

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

orthographic variation

prefixes and postfixes

CDC28 vs. Cdc28p

Myc vs. c-Myc

singular and plural forms

noun and adjective forms

flexible matching

upper- and lower-case

spaces and hyphens

disambiguation

homonyms

“black list”

unfortunate names

SDS

a

scalable implementation

>10 km<10 hours

augmented browsing

show relevant information

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

Reflect

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

web services

still too much to read

information extraction

formalize the facts

the starting point

named entity recognition

two approaches

co-mentioning

within documents

within paragraphs

within sentences

weighted counts

co-mentioning score

absolute co-mentionings

relative overrepresentation

NLPNatural Language Processing

grammatical analysis

part-of-speech tagging

noun, verb, etc.

multiword detection

semantic tagging

binding, regulation, etc.

sentence parsing

Gene and protein names

Cue words for entity recognition

Verbs for relation extraction

[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]

extract stated facts

handle negations

high precision

poor recall

highly domain specific

Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1

hyperphosphorylation and degradation

text corpora

a body of text

most use abstracts

few use full-text articles

no access

~22 mio. abstracts

~1.8 mio. free articles

~1.4 mio. Elsevier articles

~7.5 mio. patents

web resources

information on proteins

iHOP

STRING

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

text mining channel

what is known

not in databases

human proteins

co-mentioning dominates

NLP provides actions

homology transfer

STITCH

small molecules

COMPARTMENTS

subcellular localization

DISEASES

human diseases

search for a protein

search for a disease

STRING payload

evidence viewers

electronic health records

what happens at a hospital

Jensen et al., Nature Reviews Genetics, 2012

two types of data

structured data

Jensen et al., Nature Reviews Genetics, 2012

unstructured data

clinical narrative

getting access

patient consent

opt-out

opt-in

ethical approval

medical question

no explorative studies

data security

not anonymized

not transferable

hospital IT systems

not standardized

clinical narrative

not normal language

trouble for NLP

in native language

not English

few tools

no dictionaries

by busy doctors and nurses

typos

medical text mining

what is possible?

a psychiatric corpus

clinical narrative

in Danish

dictionaries

diseases

drugs

adverse drug reactions

disease comorbidity

Jensen et al., Nature Reviews Genetics, 2012

multiple testing

comorbidity matrix

Roque et al., PLoS Computational Biology, 2011

patient clustering

Jensen et al., Nature Reviews Genetics, 2012

clustering algorithm

Roque et al., PLoS Computational Biology, 2011

patient stratification

temporal correlation

drug treatment

adverse drug events

Eriksson et al., in preparation, 2012

pharmacovigilance

thank you!

questions?