title: The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research.
abstract: BACKGROUND
  Previously we generated a chronic obstructive pulmonary disease (COPD) specific knowledge base (http://www.copdknowledgebase.eu) from clinical and experimental data, text-mining results and public databases. This knowledge base allowed the retrieval of specific molecular networks together with integrated clinical and experimental data.
  
  
  RESULTS
  The COPDKB has now been extended to integrate over 40 public data sources on functional interaction (e.g. signal transduction, transcriptional regulation, protein-protein interaction, gene-disease association). In addition we integrated COPD-specific expression and co-morbidity networks connecting over 6 000 genes/proteins with physiological parameters and disease states. Three mathematical models describing different aspects of systemic effects of COPD were connected to clinical and experimental data. We have completely redesigned the technical architecture of the user interface and now provide html and web browser-based access and form-based searches. A network search enables the use of interconnecting information and the generation of disease-specific sub-networks from general knowledge. Integration with the Synergy-COPD Simulation Environment enables multi-scale integrated simulation of individual computational models while integration with a Clinical Decision Support System allows delivery into clinical practice.
  
  
  CONCLUSIONS
  The COPD Knowledge Base is the only publicly available knowledge resource dedicated to COPD and combining genetic information with molecular, physiological and clinical data as well as mathematical modelling. Its integrated analysis functions provide overviews about clinical trends and connections while its semantically mapped content enables complex analysis approaches. We plan to further extend the COPDKB by offering it as a repository to publish and semantically integrate data from relevant clinical trials. The COPDKB is freely available after registration at http://www.copdknowledgebase.eu.
authors.forename: Isaac
authors.initials: I
authors.lastname: Cano
authors.forename: Ákos
authors.initials: Á
authors.lastname: Tényi
authors.forename: Christine
authors.initials: C
authors.lastname: Schueller
authors.forename: Martin
authors.initials: M
authors.lastname: Wolff
authors.forename: M Mercedes
authors.initials: MM
authors.lastname: Huertas Migueláñez
authors.forename: David
authors.initials: D
authors.lastname: Gomez-Cabrero
authors.forename: Philipp
authors.initials: P
authors.lastname: Antczak
authors.forename: Josep
authors.initials: J
authors.lastname: Roca
authors.forename: Marta
authors.initials: M
authors.lastname: Cascante
authors.forename: Francesco
authors.initials: F
authors.lastname: Falciani
authors.forename: Dieter
authors.initials: D
authors.lastname: Maier
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D057225:Data Mining; D003628:Database Management Systems; D016208:Databases, Factual; D020000:Decision Support Systems, Clinical; D020869:Gene Expression Profiling; D006801:Humans; D051188:Knowledge Bases; D016730:Program Development; D029424:Pulmonary Disease, Chronic Obstructive / Q000235:genetics / Q000503:physiopathology* / Q000628:therapy; D012984:Software; D057170:Translational Research, Biomedical / Q000379:methods*; D014584:User-Computer Interface