Large-scale integration of data and text
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Large-scale integration of data and text
Lars Juhl Jensen
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cellular network biology
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association networks
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guilt by association
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molecular networks
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proteins
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string-db.org
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small molecules
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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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usage statistics
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heavily used
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especially in the US
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data integration
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heterogeneous data
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curated knowledge
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experimental data
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computational predictions
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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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common identifiers
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quality scores
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score calibration
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missing most of the data
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text mining
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>10 km
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named entity recognition
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comprehensive lexicon
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cyclin dependent kinase 1
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CDC2
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orthographic variation
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hCdc2
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“black list”
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SDS
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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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IDG-specific tasks
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target classification
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text mining
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“protein studiedness”
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probabilistic counting
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resource integration
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disease associations
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tissue expression
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subcellular localization
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automation of updates
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web services
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remapping of identifiers
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predictions for dark matter
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network-based inference
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questions?