The pragmatic text miner: It's just another type of poorly standardized data
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Lars Juhl Jensen
The pragmatic text miner
It’s just another type of poorly standardized data
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why text mining?
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data mining
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guilt by association
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structured data
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unstructured text
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biomedical literature
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>10 km
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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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text corpus
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comprehensive lexicon
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synonyms
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expansion rules
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prefixes and suffixes
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flexible matching
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hyphens and spaces
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“black list”
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a
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co-mentioning
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within documents
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within paragraphs
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within sentences
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weighted score
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unifying text & data
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text mining
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curated knowledge
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experimental data
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computational predictions
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integrated web resources
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protein networks
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string-db.org
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chemical networks
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stitch-db.org
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subcellular localization
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compartments.jensenlab.org
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tissue expression
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tissues.jensenlab.org
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disease associations
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many sources
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different formats
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different identifiers
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variable quality
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hard work
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collaboration model
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domain experts
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what?
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why?
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problem
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manpower
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me
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how?
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technology
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guidance
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biodiversity
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organisms
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environments
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Encyclopedia of Life
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British Heritage Library
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what we need
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the format is not important
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the license is
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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