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Integration of biomedical literature and databases
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Integration of biomedical literature and databases
Lars Juhl JensenEMBL Heidelberg
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why integration?
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why biomedicine?
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why literature?
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why databases?
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open access databases
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a lot of them
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Duncan Hull, nodalpoint.org
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PubChem
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19.2 million compounds
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GenBank
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85 million sequences
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89 billion nucleotides
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UniProt
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5.6 million sequences
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PDB
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50000 protein structures
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BINDBiomolecular Interaction Network Database
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DIPDatabase of Interacting Proteins
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MINTMolecular Interactions Database
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IntAct
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BioGRID
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204000 interactions
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too many
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incomplete
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literature mining
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MEDLINE
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17.9 million citations
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too much to read
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information retrieval
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finding the papers
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user-specified query
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“yeast AND cell cycle”
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stemming
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yeast / yeasts
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dynamic query expansion
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yeast / S. cerevisiae
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ranking
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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 it
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entity recognition
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identifying the substance(s)
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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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Cdc28 yeast
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Cdc28 cell cycle
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synonyms list
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orthographic variation
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CDC28
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Cdc28p
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disambiguation
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Cdc2
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SDS
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still too much to read
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information extraction
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formalizing the facts
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co-mentioning
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statistical methods
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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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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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yet another database
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integration
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augmented browsing
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semantic tagging
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association networks
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curated knowledge
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genomic context
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phylogenetic profiles
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gene neighborhood
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experimental data
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physical interactions
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genetic interactions
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literature mining
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restricted access
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Bayesian framework
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summary
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literature mining is good
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data integration is better
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open access
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Acknowledgments
STRING & STITCH– Christian von Mering
– Michael Kuhn
– Manuel Stark
– Samuel Chaffron
– Philippe Julien
– Tobias Doerks
– Jan Korbel
– Berend Snel
– Martijn Huynen
– Peer Bork
Reflect– Evangelos Pafilis
– Michael Kuhn
– Sean O’Donoghue
– Reinhardt Schneider
Natural Language Processing– Jasmin Saric
– Rossitza Ouzounova
– Isabel Rojas
– Peer Bork
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