From phenotype to genotype: issues in navigating the available information resources

pre-printObjectives-As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. Methods-We focused on a set of single gene diseases selected from main topics in MEDLINEplus, the NLM's principal resource focused on consumers. We used publicly available websites to investigate specific questions about the genes and gene products associated with the diseases. We also investigated questions of knowledge and data representation for the information resources and navigational issues. Results-Many online resources are available but they are complex and technical. The major challenges encountered when navigating from phenotype to genotype were (1) complexity of the data, (2) dynamic nature of the data, (3) diversity of foci and number of information resources, and (4) lack of use of standard data and knowledge representation methods. Conclusions-Three major informatics issues arise from the navigational challenges. First, the official gene names are insufficient for navigation of these web resources. Second, navigational inconsistencies arise from difficulties in determining the number and function of alternate forms of the gene or gene product and maintaining currency with this information. Third, synonymy and polysemy cause much confusion. These are severe obstacles to computational navigation from phenotype to genotype, especially for individuals who are novices in the underlying science. Tools and standards to facilitate this navigation are sorely needed

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

BACKGROUND: Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. RESULTS: Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. CONCLUSIONS: The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends

Constructing a bio-health knowledge base for access via a standardised electronic health record prototype

Aim and Objectives: To explore the feasibility of accessing biological information and associated health information through a standards-based electronic health record. The objectives include constructing: a condition specific knowledge base prototype; an EHR system prototype based on a standard record architecture; and an interface that connects the two. Method: An ontology was constructed to organise biological and health information in a formal and structured way. Cystic fibrosis was selected as an exemplar condition and the Continuity of Care Record was selected for an EHR prototype application. The sequence variations information and health information in the knowledge base are presented through the EHR prototype's interface and the results are evaluated. Results: A substantive knowledge base prototype of cystic fibrosis was constructed. The content includes: the most common genetic mutations related to cystic fibrosis; time-oriented descriptions of cystic fibrosis; Cochrane conclusions; and gene therapy for cystic fibrosis. The content is organised on both time and problem oriented axes. It was found to be possible to present bio-health information that was case-specific through the EHR prototype interface. Conclusion: Sequence variations information and associated health information can be made accessible through a standards-based electronic health record prototype. Complex knowledge can be accessed, to some extent automatically, thereby providing a starting point for integrating formal and structured biological information within health record systems which can be deployed in clinical settings.EThOS - Electronic Theses Online ServiceGBUnited Kingdo