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Nucleic Acids Research Advance Access published online on October 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp832
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database

Lynn M. Schriml1,*, Cesar Arze1, Suvarna Nadendla1, Anu Ganapathy1, Victor Felix1, Anup Mahurkar1, Katherine Phillippy2, Aaron Gussman1, Sam Angiuoli1, Elodie Ghedin3, Owen White1 and Neil Hall4

1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 2National Center for Biotechnology Information, Bethesda, MD, 3University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA and 4University of Liverpool, School of Biological Sciences, UK

*To whom correspondence should be addressed. Tel: +1 410 706 6776; Fax: +1 410 706 6756; Email: lschriml{at}som.umaryland.edu

Received August 12, 2009. Revised September 16, 2009. Accepted September 18, 2009.

The Gemina system (http://gemina.igs.umaryland.edu) identifies, standardizes and integrates the outbreak metadata for the breadth of NIAID category A–C viral and bacterial pathogens, thereby providing an investigative and surveillance tool describing the Who [Host], What [Disease, Symptom], When [Date], Where [Location] and How [Pathogen, Environmental Source, Reservoir, Transmission Method] for each pathogen. The Gemina database will provide a greater understanding of the interactions of viral and bacterial pathogens with their hosts and infectious diseases through in-depth literature text-mining, integrated outbreak metadata, outbreak surveillance tools, extensive ontology development, metadata curation and representative genomic sequence identification and standards development. The Gemina web interface provides metadata selection and retrieval of a pathogen's; Infection Systems (Pathogen, Host, Disease, Transmission Method and Anatomy) and Incidents (Location and Date) along with a hosts Age and Gender. The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.


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