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The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research.

Cano I, Tényi Á, Schueller C, Wolff M, Huertas Migueláñez MM, Gomez-Cabrero D, Antczak P, Roca J, Cascante M, Falciani F, Maier D - J Transl Med (2014)

Bottom Line: 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.Its integrated analysis functions provide overviews about clinical trends and connections while its semantically mapped content enables complex analysis approaches.

View Article: PubMed Central - HTML - PubMed

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.

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Related in: MedlinePlus

Search form. Search forms provide pre-defined selections of parameters for which thresholds can be set to retrieve data. Here the body mass index was selected to retrieve patients with corresponding values.
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Figure 4: Search form. Search forms provide pre-defined selections of parameters for which thresholds can be set to retrieve data. Here the body mass index was selected to retrieve patients with corresponding values.

Mentions: In addition to the simple browse and filter access, we implemented a set of form-based searches, which allow more direct access to information and are continuously expanded based on user feedback. Currently the search form for patient selection is based on all clinical parameters such as BMI or dyspnoea Borg scale, allowing minimum and maximum threshold values to be set (Figure 4). Other search forms allow molecular data (e.g. metabolite or protein measurements) to be retrieved.


The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research.

Cano I, Tényi Á, Schueller C, Wolff M, Huertas Migueláñez MM, Gomez-Cabrero D, Antczak P, Roca J, Cascante M, Falciani F, Maier D - J Transl Med (2014)

Search form. Search forms provide pre-defined selections of parameters for which thresholds can be set to retrieve data. Here the body mass index was selected to retrieve patients with corresponding values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4255911&req=5

Figure 4: Search form. Search forms provide pre-defined selections of parameters for which thresholds can be set to retrieve data. Here the body mass index was selected to retrieve patients with corresponding values.
Mentions: In addition to the simple browse and filter access, we implemented a set of form-based searches, which allow more direct access to information and are continuously expanded based on user feedback. Currently the search form for patient selection is based on all clinical parameters such as BMI or dyspnoea Borg scale, allowing minimum and maximum threshold values to be set (Figure 4). Other search forms allow molecular data (e.g. metabolite or protein measurements) to be retrieved.

Bottom Line: 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.Its integrated analysis functions provide overviews about clinical trends and connections while its semantically mapped content enables complex analysis approaches.

View Article: PubMed Central - HTML - PubMed

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.

Show MeSH
Related in: MedlinePlus