Download - Text mining and data integration
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Lars Juhl Jensen
Text mining and data integration
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exponential growth
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~45 seconds per paper
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information retrieval
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named entity recognition
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information extraction
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association networks
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data integration
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information retrieval
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find the relevant papers
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ad hoc retrieval
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user-specified query
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“yeast AND cell cycle”
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PubMed
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indexing
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fast lookup
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stemming
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word endings
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dynamic query expansion
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MeSH terms
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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
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no tool will find that
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named entity recognition
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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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identify the concepts
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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
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comprehensive lexicon
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CDC2
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cyclin dependent kinase 1
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orthographic variation
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upper- and lower-case
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CDC2
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Cdc2
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spaces and hyphens
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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prefixes and postfixes
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CDC2
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hCDC2
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“black list”
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SDS
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scalable implementation
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>10 km<10 hours
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augmented browsing
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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
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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
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Reflect
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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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information extraction
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formalize the facts
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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
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two approaches
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co-mentioning
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counting
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within documents
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within paragraphs
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within sentences
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co-mentioning score
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NLPNatural Language Processing
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grammatical analysis
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part-of-speech tagging
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multiword detection
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semantic tagging
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sentence parsing
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Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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extract stated facts
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high precision
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poor recall
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text corpus
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most use abstracts
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few use full-text articles
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no access
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PDF files
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layout-aware extraction
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my corpus
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~22 million abstracts
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~4 million articles
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association networks
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guilt by association
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STRING
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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computational predictions
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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gene neighborhood
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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a real example
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Cell
Cellulosomes
Cellulose
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experimental data
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gene coexpression
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physical interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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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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hard work
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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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data integration
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general approach
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suite of web resources
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STITCH
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STRING + 300k chemicals
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Kuhn et al., Nucleic Acids Research, 2012
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COMPARTMENTS
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subcellular localization
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compartments.jensenlab.org
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TISSUES
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tissue expression
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tissues.jensenlab.org
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DISEASES
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disease genes
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unification
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curated knowledge
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text mining
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experimental data
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computational predictions
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common identifiers
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quality scores
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visualization
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dissemination
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web interfaces
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evidence viewers
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web services
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diseases.jensenlab.org
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bulk download
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thank you!