The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research
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RESEARCH
Open Access
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research Isaac Cano1, Ákos Tényi1, Christine Schueller2, Martin Wolff2, M Mercedes Huertas Migueláñez3, David Gomez-Cabrero4, Philipp Antczak5, Josep Roca1,6, Marta Cascante1,7, Francesco Falciani5, Dieter Maier2*
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 subnetworks 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.
Background We previously reported the public availability of a chronic obstructive pulmonary disease (COPD) specific knowledge base [1]. This COPDKB semantically integrated existing COPD related knowledge such as genotype - phenotype relations or signal transduction pathways into structured networks that were connected with clinical and experimental data. To this end an object-oriented knowledge model was generated which contained concepts such as * Correspondence: [email protected] 2 Biomax Informatics AG, 82152, Planegg, Germany Full list of author information is available at the end of the article
“gene”, “disease” or “organ” and their associations such as “causes”, “damages”. We established a gen
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