Towards Pathway Prediction and Subcellular Localization by using FraMeTex (Workshop Abstract)

Wallmeyer T, Sommer B, Kormeier B. Towards Pathway Prediction and Subcellular Localization by using FraMeTex (Workshop Abstract). In: Sommer B, ed. Proceedings of the CELLmicrocosmos neXt workshop. Bielefeld: Bielefeld University; 2014: 18-19

GraphSAW: A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data

Shoshi A, Hoppe T, Kormeier B, Ogultarhan V, Hofestädt R. GraphSAW: A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data. BMC Medical Informatics and Decision Making. 2015;15(1): 15.Background Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. Methods The integration of database information is a promising method for providing well-based knowledge to avoid adverse drug reactions. This paper presents our web-based decision support system GraphSAW which analyzes and evaluates drug interactions and side effects based on data from two commercial and two freely available molecular databases. The system is able to analyze single and combined drug-drug interactions, drug-molecule interactions as well as single and cumulative side effects. In addition, it allows exploring associative networks of drugs, molecules, metabolic pathways, and diseases in an intuitive way. The molecular medication analysis includes the capabilities of the upper features. Results A statistical evaluation of the integrated data and top 20 drugs concerning drug interactions and side effects is performed. The results of the data analysis give an overview of all theoretically possible drug interactions and side effects. The evaluation shows a mismatch between pharmaceutical and molecular databases. The concordance of drug interactions was about 12% and 9% of drug side effects. An application case with prescribed data of 11 patients is presented in order to demonstrate the functionality of the system under real conditions. For each patient at least two interactions occured in every medication and about 8% of total diseases were possibly induced by drug therapy. Conclusions GraphSAW (http://tunicata.techfak.uni-bielefeld.de/graphsaw/ webcite) is meant to be a web-based system for health professionals and researchers. GraphSAW provides comprehensive drug-related knowledge and an improved medication analysis which may support efforts to reduce the risk of medication errors and numerous drastic side effects

Semi-automated reconstruction of biological networks based on a life science data warehouse

Kormeier B. Semi-automated reconstruction of biological networks based on a life science data warehouse. Bielefeld (Germany): Bielefeld University; 2010.The progress in the area of biological research in recent years leads to a multiplicity of different databases and information systems. Typically, those data is available via the World Wide Web for further investigation. Usually, biological and life science data that describe different aspects of a biological system are distributed and spread over the whole world. Moreover, molecular biology deals with complex problems and an enormous amount of versatile data will be produced by high-throughput techniques. Hence, the total number of databases, as well the data itself, is continuously increasing, whereas rises the distribution and heterogeneity of the data. For a comprehensive and efficient use of life science data it is necessary to integrate the distributed and heterogeneous data and provide them for further analysis to the researcher. Beside data integration the user has to be supported by applicable tools for navigation within the integrated data sets that supports an efficient and precise processing of the data. The importance of database integration has been recognized for many years. Therefore, this work describes an evolving data warehouse infrastructure for constructing life science data warehouses that integrate multiple heterogeneous biological databases within a single physical data physical database management system to facilitate queries that span multiple databases. In addition, the accurate representation of the integrated research data in a user-friendly format is highly demanded among scientists. Information must be visualized in a clear and understandable way. Otherwise important information can get lost. Therefore, a specific data warehouse approach related to cardiovascular disease and a general data warehouse approach to browse and explore life science data are presented. The systems enable intuitive search of integrated life science data, simple navigation to related information as well as visualization of biological domains and their relationships. In addition, this thesis presents a software framework for visualizing and modeling biological networks. The user is able to create a user-specific pathway without any restrictions. Moreover, the editor is connected to the data warehouse approach, so that the user can take advantage of a wide range of biomedical data sources. Additionally, an easy-to-use Web-based application for modeling of biological networks as Petri nets is motivated. The system supports semi-automatic generation of hybrid Petri net models. Then, it is possible to use generated networks in external simulation environments for qualitative and quantitative simulation. The work was funded in context of the Cardioworkbench EU project. Thus, the applications are already in use within the Cardioworkbench project as well as in ongoing in-house projects. As result, this work presents a powerful and flexible data warehouse infrastructure that can be used for building project specific information systems and data warehouses. Furthermore, the system is the basis for the network modeling application pathway reconstruction tool. Finally, this work shows the semi-automated reconstruction approach of biological network based on life science data integration supported by the developed tools within this thesis

Data Warehouses in Bioinformatics: Integration of Molecular Biological Data

Kormeier B, Hippe K, Hofestädt R. Data Warehouses in Bioinformatics: Integration of Molecular Biological Data. it Information Technology. 2011;53(5):241-249

Integrative analysis of drug interactions and side effects on pharmacological and molecular level

Shoshi A, Kormeier B, Hoppe T, Hofestädt R. Integrative analysis of drug interactions and side effects on pharmacological and molecular level. Presented at the NETTAB 2014: From structural bioinformatics to integrative systems biology, Turin

BioDWH: a data warehouse kit for life science data integration

Töpel T, Kormeier B, Klassen A, Hofestädt R. BioDWH: a data warehouse kit for life science data integration. Journal of Integrative Bioinformatics. 2008;5(2):343-349.This paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. It stands out from other approaches by providing up-to-date integrated knowledge, platform and database independence as well as high usability and customization. This open source software can be used as a general infrastructure for integrative bioinformatics research and development. The advantages of the approach are realized by using a Java-based system architecture and object-relational mapping (ORM) technology. Finally, a practical application of the system is presented within the emerging area of medical bioinformatics to show the usefulness of the approach. The BioDWH data warehouse software is available for the scientific community at http://sourceforge.net/projects/biodwh/

CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases

Kormeier B, Hippe K, Töpel T, Hofestädt R. CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases. Journal of Integrative Bioinformatics. 2010;7(1): 142

DAWIS-M.D. - A Data Warehouse System for Metabolic Data

Hippe K, Kormeier B, Töpel T, Janowski SJ, Hofestädt R. DAWIS-M.D. - A Data Warehouse System for Metabolic Data. In: Informatik 2010: Service Science - neue Perspektiven für die Informatik. LNI. Vol 176. Bonn: Ges. für Informatik; 2010: 720-725