large-scale integration of data and...
TRANSCRIPT
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Large-scale integration of data and text
Lars Juhl Jensen
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interaction networks
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association networks
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guilt by association
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protein networks
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STRING
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9.6 million proteins
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common foundation
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heterogeneous data
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curated knowledge
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(what we know)
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protein complexes
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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experimental data
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(what we measured)
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gene coexpression
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microarrays
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RNAseq
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physical interactions
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Yeast two-hybrid
Tande
m affin
ity p
urifi
catio
nProtein-fragm
ent complem
entation assay
81003P_borkjensen.eps19 by 19
Nuclear
Hydrophobic
Transmembrane
Dis
orde
red
BasicAbundant
Cytosolic
Long
0.2
0.1
Bait
Bait
Reconstitutedenzyme
Co-purifiedproteins
Prey
Prey
Bait
TAP tag
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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predictions
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(what we infer)
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genomic context
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evolution
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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gene neighborhood
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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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a real example
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Cell
Cellulosomes
Cellulose
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complications
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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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not same species
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hard work
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parsers
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mapping files
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quality scores
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affinity purification
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von Mering et al., Nucleic Acids Research, 2005
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phylogenetic profiles
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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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implicit weighting by quality
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common scale
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homology-based transfer
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orthologous groups
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Franceschini et al., Nucleic Acids Research, 2013
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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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exponential growth
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~40 seconds per paper
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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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orthographic variation
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expansion rules
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prefixes and suffixes
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CDC2
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hCdc2
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flexible matching
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spaces and hyphens
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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“black list”
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SDS
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information extraction
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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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scoring scheme
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score calibration
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NLP Natural Language Processing
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part-of-speech tagging
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what you learned in school pronoun pronoun verb preposition noun
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grammatical analysis
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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]
Saric et al., Proceedings of ACL, 2004
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summary
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association networks
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heterogeneous data
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common identifiers
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quality scores
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protein networks
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Szklarczyk et al., Nucleic Acids Research, 2015 string-db.org
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general approach
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STITCH
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chemical networks
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Kuhn et al., Nucleic Acids Research, 2014 stitch-db.org
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COMPARTMENTS
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subcellular localization
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Binder et al., Database, 2014 compartments.jensenlab.org
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TISSUES
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tissue expression
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tissues.jensenlab.org Santos et al., submitted, 2015
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DISEASES
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disease associations
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diseases.jensenlab.org Frankild et al., Methods, 2015
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questions?