mining text and data on chemicals lars juhl jensen
Post on 21-Dec-2015
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TRANSCRIPT
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Mining text and data on chemicals
Lars Juhl Jensen
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three parts
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text mining
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data integration
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medical records
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Part 1text mining
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exponential growth
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some things are constant
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~45 seconds per paper
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information retrieval
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find the relevant papers
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still too much to read
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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identify the concepts
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small molecules
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proteins
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diseases
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comprehensive lexicon
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synonyms
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orthographic variation
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“black list”
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unfortunate names
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Reflect
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augmented browsing
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browser add-on
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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Firefox
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Internet Explorer
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Google Chrome
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Safari
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Utopia Documents
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web services
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collaboration
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SciVerse
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information extraction
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formalize the facts
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co-mentioning
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NLPNatural Language Processing
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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]
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Part 2data integration
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STITCH
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Kuhn et al., Nucleic Acids Research, 2012
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~300,000 small molecules
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~2.6 million proteins
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1100+ genomes
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experimental data
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physical binding
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chemical–protein
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protein–protein
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curated knowledge
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drug targets
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complexes
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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text mining
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co-mentioning
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NLPNatural Language Processing
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many data types
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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spread over many genomes
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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probabilistic scores
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orthology transfer
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combine the evidence
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Part 3patient records
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a hard problem
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in Danish
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by busy doctors
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about psychiatric patients
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no lexicon
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acronyms
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typos
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delusions
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domain specific system
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patient record excerpt
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F20
F200
Negation
Family
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medication
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adverse drug events
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diagnoses
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pharmacovigilance
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patient stratification
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Roque et al., PLoS Computational Biology, 2011
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disease comorbidity
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Roque et al., PLoS Computational Biology, 2011
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DNA sequencing
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genotype
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phenotype
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Acknowledgments
ReflectSune FrankildHeiko HornEvangelos PafilisJuan-Carlos Silla-CastroMichael KuhnReinhardt SchneiderSean O’Donoghue
STITCHMichael KuhnDamian SzklarczykAndrea FranceschiniMilan SimonovicAlexander RothPablo MinguezTobias Doerks
Manuel StarkChristian von MeringPeer Bork
EPJ-miningFrancisco S RoquePeter B JensenRobert ErikssonHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulThomas WergeSøren Brunak
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