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At least 37 records · Page 2Linked to original sources
PubMed2001

A model for data integration systems of biomedical data applied to online genetic databases.

We present a general model for data integration systems using a mediated schema to represent commonalities in the underlying sources. These sources are mapped to the mediated schema using source descriptions. Users can pose queries against the mediated schema, allowing the system to generate automatically a query plan that enumerates and ranks all possible ways in which the query could be answered. We apply this approach to the domain of online genetic databases, demonstrating the system s ability to answer relevant queries across multiple sources.

Databases, Genetic↗
PubMed2004

A nation's genes for a cure to cancer: evolving ethical, social and legal issues regarding population genetic databases.

The advent of the human genome sequence has focused research on understanding underlying genetic links to complex diseases such as cancer, asthma and heart disease. In the past few years, individual countries, such as Iceland, Estonia, Singapore and the United Kingdom, have created national databases of their citizens' DNA for comparative research. Most recently, an international consortium including Nigeria, Japan, China and the United States launched a $100 million project called the International HapMap to map the human genome according to haplotypes, blocks of DNA that contain genetic variation. Such population genetic databases present challenging ethical, social and legal issues, yet regulation of genetic information has developed sporadically, from region to region, without a consistent international standard. Without a clear understanding of the consequences of genetic research in terms of individual and community-wide discrimination and stigmatization, genetic databases raise concerns about the protection of genetic information. This Note provides a survey of the evolving landscape of population genetic databases as a legislative and public policy tool for national and international regulators. It compares different approaches to regulating the collection and use of population genetic databases in order to understand what areas of consensus are formulating a foundation for an international standard. As the first population genetics project that will span multiple countries for the collection of DNA, the International HapMap has the potential to become an influential standard for the protection of population genetic information. This Note highlights issues among the national databases and the HapMap project that raise ethical, social and legal concerns for the future and recommends further protections for both individual donors and community interests.

Access to Information↗
PubMed1988

HGDBMS: a human genetics database management system.

Human genetics research involves a large number of complex data sets naturally organized in hierarchical structures. Data collection is performed on different levels, e.g., the project level, pedigree level, individual level, and sample level. Different aspects of a study utilize different views of the data, requiring a flexible database management system (DBMS) which satisfies these different needs for data collection and retrieval. We describe HGDBMS, a comprehensive relational DBMS, implemented as an application of the GENISYS I DBMS, which allows embedding the hierarchical structure of pedigrees in a relational structure. The system's file structure is described in detail. Currently our Melanoma and Chromosome 17 map studies are managed with HGDBMS. Our initial experience demonstrates the value of a flexible system which supports the needs for data entry, update, storage, reporting, and analysis required during different phases of genetic research. Further developments will focus on the integration of HGDBMS with a human genetics expert system shell and analysis programs.

Computer Systems↗
PubMed2006

Integration of internet-based genetic databases into the medical school pre-clinical and clinical curriculum.

Over the past several years, the field of medical genetics has continued to expand and is now impacting a broad range of medical care, mainly due to rapid advances in genetic technology and information generated by the Human Genome Project. Physicians from multiple disciplines will need to become familiar with genetic principles, and the availability of genetic databases on the internet is a valuable resource for medical students and physicians. To integrate these tools into medical student training, the University of Chicago Pritzker School of Medicine set out to develop multiple, interactive, case-based, educational sessions in the pre-clinical and clinical curriculum, designed to reinforce basic principles taught in the pre-clinical genetics class and demonstrate the usefulness of genetic information accessible via the internet in the clinical setting. Two interactive sessions and a self-assessment exercise were developed. The sessions took place in a computer classroom where each student had access to the internet and could work independently. The sessions used case-based scenarios to help students become familiar with internet based resources and demonstrate how genetic information can affect medical care. The sessions were well received by the student participants with 99% agreeing that the material was useful and important to clinical medicine. In a follow-up questionnaire 1/3 of the students reported using the databases presented during class in a clinical setting.

Computational Biology↗
PubMed2005

Lessons from European population genetic databases: comparing the law in Estonia, Iceland, Sweden and the United Kingdom.

The advent of large-scale, population genetic databases (PGDs) in several countries around the world marks a significant development in human DNA banking and genetic research. The European countries that have led the way in the development of PGDs are Iceland, Sweden, Estonia and the U.K. In legal terms, the emergence of PGDs has been far from straightforward as such projects pose a range of difficult and complex issues for the law to address. This article canvasses the current law in Iceland, Estonia, Sweden and the U.K. on four fundamental issues of principle pertaining to PGDs, in order to illustrate the difficulties that have emerged around PGDs, highlight key areas of legal concern, and shed light on possible ways forward. It compares and contrasts the differing legal positions and lawmakers' responses to date in these four European countries that have established PGDs or are seeking to do so. The four fundamental issues examined are: (1) consent, especially for secondary research purposes; (2) ownership of biological samples, data and databases; (3) the rights of certain third parties to gain access to, and to use, PGD biological samples and data; and (4) benefit sharing, including the provision of feedback and genetic counselling to participants. This analysis may offer some guidance for policymakers in other jurisdictions where PGDs have been proposed or are being established.

Databases, Genetic↗
PubMed2005

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.

The identification of genes underlying human genetic disorders requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes. In the field of human genetics, it is normal to perform this combination analysis by hand. We report on GeneSeeker (http://www.cmbi.ru.nl/GeneSeeker/), a web server that gathers and combines data from a series of databases. All database searches are performed via the web interfaces provided with the original databases, guaranteeing that the most recent data are queried, and obviating data warehousing. GeneSeeker makes the same selection of candidate genes as the human geneticists would have performed, and thus reducing the time-consuming process to a few minutes. GeneSeeker is particularly well suited for syndromes in which the disease gene displays altered expression patterns in the affected tissue(s).

Chromosome Mapping↗
PubMed1994

Mood Disorder Service Genetic Database: morbidity risks for mood disorders in 3,942 first-degree relatives of 671 index cases with single depression, recurrent depression, bipolar I, or bipolar II.

There is increasing evidence that genetic factors play a role in the etiology of mood disorders. As a result, relatives of affected individuals are more often asking about their own risks to develop a mood disorder. From 1988 to 1990, all consecutive, unrelated inpatients and outpatients (index cases) presenting to the Mood Disorders Service, Department of Psychiatry, University of British Columbia, had detailed family histories taken, thus creating the Mood Disorders Service Genetic Database. Diagnoses for index cases and their first-degree relatives were made according to Research Diagnostic Criteria and Family History Research Diagnostic Criteria respectively. Morbidity risks for mood disorders were calculated for first-degree relatives (parents, siblings, children--aged 10 and above) of all index cases with a diagnosis of single depression, recurrent depression, bipolar I, or bipolar II disorder. Morbidity risks were calculated using the maximum likelihood approach. Morbidity risk data are presented according to the sex and diagnosis for the index case in an easy reference format for risk counselling. The risks are presented twice, including and excluding data for "high-risk" families whose genetic pedigree is suggestive of "autosomal dominant" inheritance.

Age of Onset↗
PubMed2002

Social benefits of non-criminal genetic databases: missing persons and human remains identification.

A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.

Cadaver↗
PubMed2006

Genetic databases and pharmacogenetics: introduction.

Since the inception of the Human Genome Project, human genetics has frequently been conducted through big science projects, combining academic, state and industrial methods, interests and resources. The legitimacy of such projects has been linked to national prestige and images of the nation, the purity of scientific endeavour, the entrepreneurial spirit, medical progress and the public health. A key complication in these discourses is that large-scale genetic research has yet to show major results when considered in terms of the objectives used to legitimate investment and social support for these projects. The main area showing promise at present is the developing field of pharmacogenetics, which is now attracting major industry and government investment. Sociological, ethical and philosophical study of human genetic sample-based research and pharmacogenetics has developed in parallel with inquiry in the biological and biomedical sciences. This paper introduces a symposium on the ethical and social aspects of this field of biomedical research.

Databases, Genetic↗
PubMed1997

Informatics--genome and genetic databases.

Databases for biologists are becoming increasingly important. Some of these can be regarded as 'core' resources, such as the bibliographic databases, whereas others are of greater interest to specialists. As comparative genomics develops, however, even databases limited in their scope (e.g. to a single organism) are of great interest to a wider community.

Animals↗