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

L. M. Schriml, C. Arze, S. Nadendla, A. Ganapathy, V. Felix, A. Mahurkar, K. Phillippy, A. Gussman, S. Angiuoli, E. Ghedin, O. White, N. Hall
2009 Nucleic Acids Research  
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  ...  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  ...  ACKNOWLEDGEMENTS The authors thank Matthew Davenport for his continue guidance and support of the Gemina project.  ... 
doi:10.1093/nar/gkp832 pmid:19850722 pmcid:PMC2808878 fatcat:y4pap3wjqbaazhacqwrpu2k754

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

S.M.Shamimul Hasan, Edward A. Fox, Keith Bisset, Madhav V. Marathe
2017 Journal of Healthcare Informatics Research  
EpiK is designed to support agent-based modeling and analytics frameworks-aggregate models can be seen as special cases and are thus supported.  ...  As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets.  ...  Schriml et al. provide the GeMIna system, that uses epidemiology metadata to identify infectious pathogens and their representative genomic sequences [57].  ... 
doi:10.1007/s41666-017-0010-9 pmid:35415398 pmcid:PMC8982844 fatcat:m5d3lglydfh27pcdbx22icguay

Augmenting spatio-textual search with an infectious disease ontology

Michael D. Lieberman, Jagan Sankaranarayanan, Hanan Samet, Jon Sperling
2008 2008 IEEE 24th International Conference on Data Engineering Workshop  
It identifies references to infectious diseases by using a disease ontology.  ...  A system is described that automatically categorizes and classifies infectious disease incidence reports by type and geographic location, to aid analysis by domain experts.  ...  The authors wish to thank Adam Phillippy for his help with the ontology tagging module.  ... 
doi:10.1109/icdew.2008.4498330 dblp:conf/icde/LiebermanSSS08 fatcat:tztpjwfxfbeu5ekrkfujut6gp4

The environment ontology: contextualising biological and biomedical entities

Pier Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall, Suzanna E Lewis
2013 Journal of Biomedical Semantics  
The Environment Ontology (ENVO; is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science  ...  disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes.  ...  For example, the Genomic Metadata for Infectious Agents Database (GEMINA; [53] ) supports queries using ENVO classes, and the National Institute for Allergy and Infectious Diseases (NIAID) Bioinformatics  ... 
doi:10.1186/2041-1480-4-43 pmid:24330602 pmcid:PMC3904460 fatcat:boxqxyq2pnen3nzboofx2dvsd4