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The STITCH and Reflect web resources
 

The STITCH and Reflect web resources

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Workshop on Drug Discovery Informatics, Technical University of Denmark, Lyngby, Denmark, January 26, 2010.

Workshop on Drug Discovery Informatics, Technical University of Denmark, Lyngby, Denmark, January 26, 2010.

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  • This is a conservative estimate based only on what is in PubMed Too much to read! Text mining used to extract relations Similar methods used to mine medical records and link diseases

The STITCH and Reflect web resources The STITCH and Reflect web resources Presentation Transcript

  • The STITCH and Reflect web resources Lars Juhl Jensen
  • STITCH
  • Kuhn et al., Nucleic Acids Research , 2010
  • REST web service
  • bulk download
  • parts lists
  • 630 genomes
  • >2.5 million proteins
  • many databases
  • different formats
  • model organism databases
  • Ensembl
  • RefSeq
  • PubChem compounds
  • >74,000 small molecules
  • curated knowledge
  • complexes
  • pathways
  • Letunic & Bork, Trends in Biochemical Sciences , 2008
  • high confidence
  • many databases
  • MIPS Munich Information center for Protein Sequences
  • Gene Ontology
  • KEGG Kyoto Encyclopedia of Genes and Genomes
  • MetaCyc
  • PID NCI-Nature Pathway Interaction Database
  • Reactome
  • different formats
  • different identifiers
  • partially redundant
  • interaction data
  • protein–small molecule
  • in vitro binding assays
  • protein–protein
  • yeast two-hybrid
  • affinity purification
  • fragment complementation
  • Jensen & Bork, Science , 2008
  • genetic interactions
  • Beyer et al., Nature Reviews Genetics , 2007
  • gene coexpression
  •  
  • many databases
  • BindingDB
  • CTD Comparative Toxicogenomics Database
  • DrugBank
  • GLIDA GPCR-Ligand Database
  • PDSP K i Psycoactive Drug Screening Program
  • PharmGKB Pharmacogenomics Knowledge Base
  • BIND Biomolecular Interaction Network Database
  • BioGRID General Repository for Interaction Datasets
  • DIP Database of Interacting Proteins
  • IntAct
  • MINT Molecular Interactions Database
  • HPRD Human Protein Reference Database
  • PDB Protein Data Bank
  • GEO Gene Expression Omnibus
  • different formats
  • different identifiers
  • partially redundant
  • literature mining
  • >10 km
  • human readable
  • not computer readable
  • different names
  • text corpus
  • M EDLINE
  • SGD Saccharomyces Genome Database
  • The Interactive Fly
  • OMIM Online Mendelian Inheritance in Man
  • dictionary
  • co-mentioning
  • NLP Natural Language Processing
  •  
  • restricted access
  • Reflect
  • augmented browsing
  • browser add-on
  • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  • web interface
  •  
  • REST web service
  • SOAP web service
  • collaborate publishers
  •  
  • genomic context
  • gene fusion
  • Korbel et al., Nature Biotechnology , 2004
  • conserved neighborhood
  • operons
  • Korbel et al., Nature Biotechnology , 2004
  • bidirectional promoters
  • Korbel et al., Nature Biotechnology , 2004
  • phylogenetic profiles
  • Korbel et al., Nature Biotechnology , 2004
  • integration
  • many data types
  • not comparable
  • variable quality
  • spread over 630 genomes
  • quality scores
  • calibrate vs. gold standard
  • von Mering et al., Nucleic Acids Research , 2005
  • probabilistic scores
  • orthology transfer
  • von Mering et al., Nucleic Acids Research , 2005
  • combine all evidence
  •  
  • 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
  • larsjuhljensen