A Marketplace for Ontologies and Ontology-Based Tools and Applications in the Life Sciences

This paper describes a strategy for the development of ontologies in the life sciences, tools to support the creation and use of those ontologies, and a framework whereby these ontologies can support the development of commercial applications within the field. At the core of these efforts is the need for an organization that will provide a focus for ontology work that will engage researchers as well as drive forward the commercial aspects of this effort

Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support

In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with clinical data, to support clinical decision-making by: 1) analyzing clinically relevant knowledge contained in PGx knowledge resources; 2) evaluating the feasibility of a rule-based framework to support formal representation of clinically relevant knowledge contained in PGx knowledge resources; and, 3) evaluating the ability of an electronic medical record/electronic health record (EMR/EHR) to provide computable forms of clinical data needed for PGx clinical decision support. Findings suggest that the PharmGKB is a good source for PGx knowledge to supplement information contained in FDA approved drug labels. Furthermore, we found that with supporting knowledge (e.g. IF age <18 THEN patient is a child), sufficient clinical data exists in University of Washington’s EMR systems to support 50% of PGx knowledge contained in drug labels that could be expressed as rules

Distribution of immunodeficiency fact files with XML – from Web to WAP

BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at . A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at

Six Year Refractive Change among White Children and Young Adults: Evidence for Significant Increase in Myopia among White UK Children

OBJECTIVE:To determine six-year spherical refractive error change among white children and young adults in the UK and evaluate differences in refractive profiles between contemporary Australian children and historical UK data. DESIGN:Population-based prospective study. PARTICIPANTS:The Northern Ireland Childhood Errors of Refraction (NICER) study Phase 1 examined 1068 children in two cohorts aged 6-7 years and 12-13 years. Prospective data for six-year follow-up (Phase 3) are available for 212 12-13 year olds and 226 18-20 year olds in each cohort respectively. METHODS:Cycloplegic refractive error was determined using binocular open-field autorefraction (Shin-Nippon NVision-K 5001, cyclopentolate 1%). Participants were defined by spherical equivalent refraction (SER) as myopic SER ≤-0.50D, emmetropic -0.50D<SER<+2.00 or hyperopic SER≥+2.00D. MAIN OUTCOME MEASURES:Proportion and incidence of myopia. RESULTS:The proportion of myopes significantly increased between 6-7 years (1.9%) and 12-13 years (14.6%) (p<0.001) but not between 12-13 and 18-20 years (16.4% to 18.6%, p = 0.51). The estimated annual incidence of myopia was 2.2% and 0.7% for the younger and older cohorts respectively. There were significantly more myopic children in the UK at age 12-13 years in the NICER study (16.4%) than reported in Australia (4.4%) (p<0.001). However by 17 years the proportion of myopia neared equivalence in the two populations (NICER 18.6%, Australia 17.7%, p = 0.75). The proportion of myopic children aged 12-13 years in the present study (2006-2008) was 16.4%, significantly greater than that reported for children aged 10-16 years in the 1960's (7.2%, p = 0.01). The proportion of hyperopes in the younger NICER cohort decreased significantly over the six year period (from 21.7% to 14.2%, p = 0.04). Hyperopes with SER ≥+3.50D in both NICER age cohorts demonstrated persistent hyperopia. CONCLUSIONS:The incidence and proportion of myopia are relatively low in this contemporary white UK population in comparison to other worldwide studies. The proportion of myopes in the UK has more than doubled over the last 50 years in children aged between 10-16 years and children are becoming myopic at a younger age. Differences between the proportion of myopes in the UK and in Australia apparent at 12-13 years were eliminated by 17 years of age

CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record

Objective Clinicians’ ability to use and interpret genetic information depends upon how those data are displayed in electronic health records (EHRs). There is a critical need to develop systems to effectively display genetic information in EHRs and augment clinical decision support (CDS)

Rise and Demise of Bioinformatics? Promise and Progress

The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine