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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

BioXM module structure. The modular BioXM architecture decouples tasks such as authorisation and access control from data management, search and reporting. The dynamic semantic knowledge model defines which objects and associations can be represented and analysed. Selecting from multiple "App" functions a highly specific browser-based user interface can be generated within the Foswiki open source framework.
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Figure 1: BioXM module structure. The modular BioXM architecture decouples tasks such as authorisation and access control from data management, search and reporting. The dynamic semantic knowledge model defines which objects and associations can be represented and analysed. Selecting from multiple "App" functions a highly specific browser-based user interface can be generated within the Foswiki open source framework.

Mentions: The requirement specification used elicitation methods such as user observations, focus groups, interviews and workshops to establish the use cases and workflows, which were refined based on a prototyping approach applying agile development methods. The architecture design approach followed the ISO/IEC 42010:2007 standard. Implementation of the user interface framework is based on the open source Foswiki framework (http://www.foswiki.org) for which a plugin was developed to connect the BioXM™ Knowledge Management Environment. While details of the technical architecture of BioXM have been reported elsewhere [3] we briefly summarise it here to aid understanding. As depicted in Figure 1 BioXM is implemented as a platform-independent Java client-server application with modular architecture and a relational database management system backend. The Foswiki plugin calls a dedicated servlet deployed in an Apache Tomcat servlet container. 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. A BioXM SOAP web service is used to interoperate with external applications such as the Clinical Decision Support System (CDSS) and Simulation Environment (SE). Data analyses methods are based on R scripts, which the BioXM R-plugin calls and presents the results directly in the user interface. Based on this plugin, content displayed in the browser can be dynamically generated from the knowledge base repository. The resulting user interface was iteratively validated and refined by focus groups of biomedical researchers within the Synergy-COPD projects as well as biohealth research students during two subsequent summer schools of the Erasmus Mundus BioHealth Computing program (see [4] ).


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)

BioXM module structure. The modular BioXM architecture decouples tasks such as authorisation and access control from data management, search and reporting. The dynamic semantic knowledge model defines which objects and associations can be represented and analysed. Selecting from multiple "App" functions a highly specific browser-based user interface can be generated within the Foswiki open source framework.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: BioXM module structure. The modular BioXM architecture decouples tasks such as authorisation and access control from data management, search and reporting. The dynamic semantic knowledge model defines which objects and associations can be represented and analysed. Selecting from multiple "App" functions a highly specific browser-based user interface can be generated within the Foswiki open source framework.
Mentions: The requirement specification used elicitation methods such as user observations, focus groups, interviews and workshops to establish the use cases and workflows, which were refined based on a prototyping approach applying agile development methods. The architecture design approach followed the ISO/IEC 42010:2007 standard. Implementation of the user interface framework is based on the open source Foswiki framework (http://www.foswiki.org) for which a plugin was developed to connect the BioXM™ Knowledge Management Environment. While details of the technical architecture of BioXM have been reported elsewhere [3] we briefly summarise it here to aid understanding. As depicted in Figure 1 BioXM is implemented as a platform-independent Java client-server application with modular architecture and a relational database management system backend. The Foswiki plugin calls a dedicated servlet deployed in an Apache Tomcat servlet container. 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. A BioXM SOAP web service is used to interoperate with external applications such as the Clinical Decision Support System (CDSS) and Simulation Environment (SE). Data analyses methods are based on R scripts, which the BioXM R-plugin calls and presents the results directly in the user interface. Based on this plugin, content displayed in the browser can be dynamically generated from the knowledge base repository. The resulting user interface was iteratively validated and refined by focus groups of biomedical researchers within the Synergy-COPD projects as well as biohealth research students during two subsequent summer schools of the Erasmus Mundus BioHealth Computing program (see [4] ).

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