An open-source, integrated pedigree data management and visualization tool for genetic epidemiology

An open-source, integrated pedigree data management and visualization tool for genetic epidemiology AbstractWith advances in genetic epidemiology, increasingly large amounts of pedigree-related information are being collected by family studies, including twin studies. To date, biomedical data management systems that cater for family data have usually done so as part of their standard (non-family-centric) data model. Consequently, data managers with computing expertise are needed to extract family datasets and perform family-centric operations. We present a robust approach to handling large family datasets. Our approach is implemented as a new module which extends the capabilities of The Ark, an open-source web-based biomedical data management tool. Using an algorithm designed by the authors, the pedigree module dynamically infers family relationships for any selected subject (not necessarily the proband). A web interface allows researchers to create, update, delete and navigate parental and twin relationships between subjects, and bulk import/export pedigrees. Consanguineous relationships can be captured, and configurable pedigree visualizations generated. A web services interface provides interoperability. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png International Journal of Epidemiology Oxford University Press

An open-source, integrated pedigree data management and visualization tool for genetic epidemiology

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Publisher
Oxford University Press
Copyright
© The Author(s) 2018; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association
ISSN
0300-5771
eISSN
1464-3685
D.O.I.
10.1093/ije/dyy049
Publisher site
See Article on Publisher Site

Abstract

AbstractWith advances in genetic epidemiology, increasingly large amounts of pedigree-related information are being collected by family studies, including twin studies. To date, biomedical data management systems that cater for family data have usually done so as part of their standard (non-family-centric) data model. Consequently, data managers with computing expertise are needed to extract family datasets and perform family-centric operations. We present a robust approach to handling large family datasets. Our approach is implemented as a new module which extends the capabilities of The Ark, an open-source web-based biomedical data management tool. Using an algorithm designed by the authors, the pedigree module dynamically infers family relationships for any selected subject (not necessarily the proband). A web interface allows researchers to create, update, delete and navigate parental and twin relationships between subjects, and bulk import/export pedigrees. Consanguineous relationships can be captured, and configurable pedigree visualizations generated. A web services interface provides interoperability.

Journal

International Journal of EpidemiologyOxford University Press

Published: Aug 1, 2018

References

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