Integration of heterogeneous data
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Integration of heterogeneous data
Lars Juhl Jensen
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data mining
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text mining
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interaction networks
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Kuhn et al., Nucleic Acids Research, 2010
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parts lists
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630 genomes
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2.5 million proteins
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~74,000 small molecules
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many databases
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different formats
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model organism databases
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Ensembl
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RefSeq
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PubChem
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genomic context
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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conserved neighborhood
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operons
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Korbel et al., Nature Biotechnology, 2004
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bidirectional promoters
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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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experimental data
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gene coexpression
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protein interactions
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Jensen & Bork, Science, 2008
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genetic interactions
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Beyer et al., Nature Reviews Genetics, 2007
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small molecule interactions
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in vitro binding assays
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cellular activity assays
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many databases
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GEOGene Expression Omnibus
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BINDBiomolecular Interaction Network Database
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BioGRIDGeneral Repository for Interaction Datasets
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DIPDatabase of Interacting Proteins
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IntAct
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MINTMolecular Interactions Database
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HPRDHuman Protein Reference Database
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PDBProtein Data Bank
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BindingDB
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CTDComparative Toxicogenomics Database
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DrugBank
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GLIDAGPCR-Ligand Database
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MATADOR
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PDSP KiPsycoactive Drug Screening Program
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PharmGKBPharmacogenomics Knowledge Base
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different formats
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different identifiers
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partially redundant
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Campillos & Kuhn et al., Science, 2008
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curated knowledge
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complexes
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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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Gene Ontology
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MIPSMunich Information center
for Protein Sequences
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KEGGKyoto Encyclopedia of Genes and Genomes
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MetaCyc
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Reactome
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PIDNCI-Nature Pathway Interaction Database
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high confidence
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different formats
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different identifiers
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partially redundant
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literature mining
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>10 km
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human readable
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not computer readable
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different names
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text corpus
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MEDLINE
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SGDSaccharomyces Genome Database
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The Interactive Fly
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OMIMOnline Mendelian Inheritance in Man
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thesaurus
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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 namesCue words for entity recognitionVerbs for relation extraction
[nxgene The GAL4 gene]
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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restricted access
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Reflect
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augmented browsing
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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integration
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the easy problems
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many databases
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different formats
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different identifiers
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partially redundant
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parsers
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thesaurus
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book keeping
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the hard problems
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many data types
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not comparable
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variable quality
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raw quality scores
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intergenic distances
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Korbel et al., Nature Biotechnology, 2004
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correlations
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reproducibility
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von Mering et al., Nucleic Acids Research, 2005
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score calibration
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gold standard
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von Mering et al., Nucleic Acids Research, 2005
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spread over 630 genomes
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transfer by orthology
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von Mering et al., Nucleic Acids Research, 2005
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two modes
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COG mode
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von Mering et al., Nucleic Acids Research, 2005
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protein mode
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von Mering et al., Nucleic Acids Research, 2005
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combine all evidence
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P = 1-(1-P1)(1-P2)(1-P3) …
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visualize
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Kuhn et al., Nucleic Acids Research, 2010
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access
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access for humans
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web interfaces
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access for computers
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web services
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RESTRepresentational State Transfer
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SOAPSimple Object Access Protocol
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Acknowledgments
STITCH– Michael Kuhn
– Damian Szklarczyk
– Andrea Franceschini
– Monica Campillos
– Christian von Mering
– Lars Juhl Jensen
– Andreas Beyer
– Peer Bork
Reflect– Sean O’Donoghue
– Heiko Horn
– Sune Frankild
– Evangelos Pafilis
– Michael Kuhn
– Nigel Brown
– Reinhardt Schneider
STRING– Christian von Mering
– Michael Kuhn
– Manuel Stark
– Samuel Chaffron
– Chris Creevey
– Jean Muller
– Tobias Doerks
– Philippe Julien
– Alexander Roth
– Milan Simonovic
– Jan Korbel
– Berend Snel
– Martijn Huynen
– Peer Bork
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larsjuhljensen