turning big data and text collections into web resrouces
TRANSCRIPT
![Page 1: Turning big data and text collections into web resrouces](https://reader033.vdocuments.mx/reader033/viewer/2022052618/554e8a1ab4c90573338b49ab/html5/thumbnails/1.jpg)
Lars Juhl Jensen
Turning big data and text collections into web
resources
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three parts
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data integration
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text mining
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interface design
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data integration
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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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experimental data
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physical interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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metabolic 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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missing most of the data
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text mining
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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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comprehensive lexicon
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cyclin dependent kinase 1
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CDC2
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expansion rules
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flexible matching
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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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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proteins
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small molecules
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compartments
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tissues
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diseases
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information extraction
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count co-mentioning
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within documents
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within paragraphs
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within sentences
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corpora
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~22 million abstracts
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no access
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~4 million full-text articles
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interface design
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ease of use
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web resources
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simple search interface
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complex relational database
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attractiveness
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data visualization
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STRING
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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payload
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compartments.jensenlab.org
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COMPARTMENTS
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compartments.jensenlab.org
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TISSUES
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tissues.jensenlab.org
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provenance
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evidence viewers
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DISEASES
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reusability
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web services
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download files
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open licenses
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Acknowledgments
Protein networks
Christian von MeringDamian Szklarczyk
Michael KuhnManuel Stark
Samuel ChaffronChris Creevey
Jean MullerTobias DoerksPhilippe Julien
Alexander RothMilan Simonovic
Jan KorbelBerend Snel
Martijn HuynenPeer Bork
Literature miningSune FrankildEvangelos PafilisJanos BinderKalliopi TsafouAlberto SantosHeiko HornMichael KuhnNigel BrownReinhardt SchneiderSean O’Donoghue