Abstract
BackgroundPreviously 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.ResultsThe 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.ConclusionsThe 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.
Highlights
We generated a chronic obstructive pulmonary disease (COPD) specific knowledge base from clinical and experimental data, text-mining results and public databases
We previously reported the public availability of a chronic obstructive pulmonary disease (COPD) specific knowledge base [1]
The servlet connects to different BioXM application server programming interfaces (APIs) to execute searches and retrieve pre-defined reports through the wiki plugin into an html user interface which is accessible by any modern web-browser
Summary
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. 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. Validation with user groups showed that to enable application by clinical researchers, a significant simplification of the user interface was required
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