Bioinformatics for Transporter Pharmacogenomics and Systems Biology: Data Integration and Modeling with UML

Abstract

Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

Business Process Modelling is an Essential Part of a Requirements Analysis

“…The UML alternatives are either to develop a domain model or use UML state-machine or f inite state machine diagrams . Business architecture models (BAM) have been applied to the life sciences to help generate UML models [59]; and other tailored packages have been used to generate UML diagrams for bioinformatics research [60] and to generate genotypephenotype maps [61].…”

Uncertainty Modeling of Object-Oriented Biomedical Information in HBase

“…In current computer science and medicine fields, since the notion of object and class is ubiquitous in many real-world applications, there is a paradigm shift to the object orientation in the formalisms for representations of the structured knowledge used both in knowledge representations and in databases. Object-oriented databases (OODBs) are widely used for supporting advanced database applications [1] such as such as the systems biology modeling [2], the objectoriented biomedical continuous system modeling [3], and object-oriented user interfaces for the bioinformatics analysis pipeline systems [4]. An object-oriented knowledge base [5] called SENEX is developed for modeling and representing the biomedical information about the neurodegeneration and loss of memory in aging.…”

Rosen's (M,R) system in Unified Modelling Language

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