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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

Software architecture. Integrative UML-like diagram representing the organisational, infrastructural and informational view of the software architecture. All modules communicate based on WebServices. The COPDKB provides information of type model, model paramters, parameter values (summarised as "simulation knowledge") and experimental data to the SE. The SE feeds back simulation results. With the CDSS the COPDKB exchanges requests for information on knowledge about co-morbidities and drug-interactions and provides corresponding search results. COPDKB = COPD Knowledge Base, SE = Simulation Environment, CDSS = Clinical Decision Support System, API = Application Programming Interface.
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Figure 3: Software architecture. Integrative UML-like diagram representing the organisational, infrastructural and informational view of the software architecture. All modules communicate based on WebServices. The COPDKB provides information of type model, model paramters, parameter values (summarised as "simulation knowledge") and experimental data to the SE. The SE feeds back simulation results. With the CDSS the COPDKB exchanges requests for information on knowledge about co-morbidities and drug-interactions and provides corresponding search results. COPDKB = COPD Knowledge Base, SE = Simulation Environment, CDSS = Clinical Decision Support System, API = Application Programming Interface.

Mentions: In addition to the semantic description of different types of knowledge and data, we therefore generated a technical integration between the three compounds required for integrative simulation and clinical decision support, the COPDKB, the Simulation Environment (SE, [5]) and Clinical Decision Support System (CDSS, [11]). We generated an architecture meta-model consisting of the following concepts: software components, graphical user interface (GUI), application programming interface (API), data types and information flow. Figure 3 shows an integrative UML-type diagram of the organisational, infrastructural and informational architecture views depicting the involved software components, their APIs and the information flows between them.


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)

Software architecture. Integrative UML-like diagram representing the organisational, infrastructural and informational view of the software architecture. All modules communicate based on WebServices. The COPDKB provides information of type model, model paramters, parameter values (summarised as "simulation knowledge") and experimental data to the SE. The SE feeds back simulation results. With the CDSS the COPDKB exchanges requests for information on knowledge about co-morbidities and drug-interactions and provides corresponding search results. COPDKB = COPD Knowledge Base, SE = Simulation Environment, CDSS = Clinical Decision Support System, API = Application Programming Interface.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Software architecture. Integrative UML-like diagram representing the organisational, infrastructural and informational view of the software architecture. All modules communicate based on WebServices. The COPDKB provides information of type model, model paramters, parameter values (summarised as "simulation knowledge") and experimental data to the SE. The SE feeds back simulation results. With the CDSS the COPDKB exchanges requests for information on knowledge about co-morbidities and drug-interactions and provides corresponding search results. COPDKB = COPD Knowledge Base, SE = Simulation Environment, CDSS = Clinical Decision Support System, API = Application Programming Interface.
Mentions: In addition to the semantic description of different types of knowledge and data, we therefore generated a technical integration between the three compounds required for integrative simulation and clinical decision support, the COPDKB, the Simulation Environment (SE, [5]) and Clinical Decision Support System (CDSS, [11]). We generated an architecture meta-model consisting of the following concepts: software components, graphical user interface (GUI), application programming interface (API), data types and information flow. Figure 3 shows an integrative UML-type diagram of the organisational, infrastructural and informational architecture views depicting the involved software components, their APIs and the information flows between them.

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