Please use this identifier to cite or link to this item: http://hdl.handle.net/2445/98841
Title: The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research
Author: Cano Franco, Isaac
Tényi, Ákos
Schueller, Christine
Wolff, Martin
Huertas Migueláñez , M.Mercedes
Gomez-Cabrero, David
Antczak, Philipp
Roca Torrent, Josep
Cascante i Serratosa, Marta
Falciani, Francesco
Maier, Dieter
Keywords: Malalties pulmonars obstructives cròniques
Bioinformàtica
Genètica mèdica
Investigació mèdica
Chronic obstructive pulmonary diseases
Bioinformatics
Medical genetics
Medicine research
Issue Date: 28-Nov-2014
Publisher: BioMed Central
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.
Note: Reproducció del document publicat a: http://dx.doi.org/10.1186/1479-5876-12-S2-S6
It is part of: Journal of Translational Medicine, 2014, vol. 12, num. Suppl 2, p. S6
Related resource: http://dx.doi.org/10.1186/1479-5876-12-S2-S6
URI: http://hdl.handle.net/2445/98841
ISSN: 1479-5876
Appears in Collections:Articles publicats en revistes (Medicina)

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