Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jan 17;5(1):4.
doi: 10.1186/2041-1480-5-4.

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources

Catia Pesquita  1 , João D Ferreira, Francisco M Couto, Mário J Silva
Affiliations

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources

Catia Pesquita et al. J Biomed Semantics. .

Abstract

Background: Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic annotation of epidemiology resources is a cornerstone to effectively support such activities. Although several ontologies cover some of the subdomains of epidemiology, we identified a lack of semantic resources for epidemiology-specific terms. This paper addresses this need by proposing the Epidemiology Ontology (EPO) and by describing its integration with other related ontologies into a semantic enabled platform for sharing epidemiology resources.

Results: The EPO follows the OBO Foundry guidelines and uses the Basic Formal Ontology (BFO) as an upper ontology. The first version of EPO models several epidemiology and demography parameters as well as transmission of infection processes, participants and related procedures. It currently has nearly 200 classes and is designed to support the semantic annotation of epidemiology resources and data integration, as well as information retrieval and knowledge discovery activities.

Conclusions: EPO is under active development and is freely available at https://code.google.com/p/epidemiology-ontology/. We believe that the annotation of epidemiology resources with EPO will help researchers to gain a better understanding of global epidemiological events by enhancing data integration and sharing.

PubMed Disclaimer

Figures

Figure 1
Figure 1
A representative portion of EPO. This diagram represents a portion of EPO and how EPO classes are related to each other and to other ontologies classes. Unlabeled arrows represent subclass relationships, and labeled arrows represent relations imported from RO. The ontology for each class is identified by its prefix.
Figure 2
Figure 2
A subgraph of EPO dedicated to epidemiological and demographic parameters. This diagram represents a few classes of the epidemiological and demographic parameters branches of EPO, particularly some classes with similar labels.
Figure 3
Figure 3
Annotation of sentences from scientific papers with EPO classes. This diagram exemplifies the usage of some of the EPO classes represented in Figure 4 to annotate entities mentioned in sentences extracted from scientific papers. ([1] Lessler J, Metcalf CJE, PLoS One 2013, 8, no. 7: e67639; [2] Kumar S et al., Am J Publ Heal 2013, 0: e1-e6.; [3] Nagao Y, PloS One 2013, 8, no. 7: e67934.)
Figure 4
Figure 4
Annotating an epidemiological resource with EPO using the online form of the Epidemic Marketplace. The resource in this example is annotated with one EPO class, ‘proportional mortality odds-ratio’ , and another suitable class is being searched for by inputting the word ‘incidence’. The EM returns all entries in EPO with the word ‘incidence’ and the user can see their definitions in order to choose the best alternative.
See this image and copyright information in PMC

References

    1. Porta MS. Dictionary of Epidemiology. USA: Oxford University Press; 2008.
    1. Salathé M, Bengtsson L, Bodnar TJ, Brewer DD, Brownstein JS, Buckee C. et al.Digital epidemiology. PLoS Comput Biol. 2012;8(7):e1002616. doi: 10.1371/journal.pcbi.1002616. - DOI - PMC - PubMed
    1. Broeck WV, Gioannini C, Gonçalves B, Quaggiotto M, Colizza V, Vespignani A. The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale. BMC Infect Dis. 2011;11(1):37. doi: 10.1186/1471-2334-11-37. - DOI - PMC - PubMed
    1. Chao DL, Halloran ME, Obenchain VJ, Longini IM. FluTE, a publicly available stochastic influenza epidemic simulation model. PLoS Comput Biol. 2010;6(1):e1000656. doi: 10.1371/journal.pcbi.1000656. - DOI - PMC - PubMed
    1. Tolle KM, Tansley D, Hey AJG. The Fourth Paradigm: Data-Intensive Scientific Discovery [Point of View] Proceedings of the IEEE. 2011;99(8):1334–1337.

LinkOut - more resources