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

Lynn M. Schriml, Cesar Arze, Suvarna Nadendla, Anu Ganapathy, Victor Felix, Anup Mahurkar, Katherine Phillippy, Aaron Gussman, Sam Angiuoli, Elodie Ghedin, Owen White, Neil Hall

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article numbergkp832
Pages (from-to)D754-D764
JournalNucleic acids research
Volume38
Issue numberSUPPL.1
DOIs
StatePublished - Oct 22 2009

ASJC Scopus subject areas

  • Genetics

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