Ontology for vector surveillance and management

Saul Lozano-Fuentes, Aritra Bandyopadhyay, Lindsay G. Cowell, Albert Goldfain, Lars Eisen

Research output: Contribution to journalReview article

6 Scopus citations

Abstract

Ontologies, which are made up by standardized and defined controlled vocabulary terms and their interrelationships, are comprehensive and readily searchable repositories for knowledge in a given domain. The Open Biomedical Ontologies (OBO) Foundry was initiated in 2001 with the aims of becoming an "umbrella" for life-science ontologies and promoting the use of ontology development best practices. A software application (OBO-Edit; *.obo file format) was developed to facilitate ontology development and editing. TheOBOFoundry now comprises over 100 ontologies and candidate ontologies, including the NCBI organismal classification ontology (NCBITaxon), the Mosquito Insecticide Resistance Ontology (MIRO), the Infectious Disease Ontology (IDO), theIDOMALmalaria ontology, and ontologies for mosquito gross anatomy and tick gross anatomy. We previously developed a disease data management system for dengue and malaria control programs, which incorporated a set of information trees built upon ontological principles, including a "term tree" to promote the use of standardized terms. In the course of doing so, we realized that there were substantial gaps in existing ontologies with regards to concepts, processes, and, especially, physical entities (e.g., vector species, pathogen species, and vector surveillance and management equipment) in the domain of surveillance and management of vectors and vector-borne pathogens. We therefore produced an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. The Vector Surveillance and Management Ontology (VSMO) includes >2,200 unique terms, of which the vast majority (>80%) were newly generated during the development of this ontology. One core feature of the VSMO is the linkage, through the has vector relation, of arthropod species to the pathogenic microorganisms for which they serve as biological vectors. We also recognized and addressed a potential roadblock for use of the VSMO by the vector-borne disease community: the difficulty in extracting information from OBO-Edit ontology files (*.obo files) and exporting the information to other file formats. A novel ontology explorer tool was developed to facilitate extractionandexport of information fromtheVSMO*.obo file into lists of termsandtheirassociated unique IDs in *.txt or *.csv file formats. These lists can then be imported into a database or data management system for use as select lists with predefined terms. This is an important step to ensure that the knowledge contained in our ontology can be put into practical use.

Original languageEnglish (US)
Pages (from-to)1-14
Number of pages14
JournalJournal of Medical Entomology
Volume50
Issue number1
DOIs
StatePublished - Jan 2013

Keywords

  • Management
  • Ontology
  • Pathogen
  • Surveillance
  • Vector

ASJC Scopus subject areas

  • Parasitology
  • veterinary(all)
  • Insect Science
  • Infectious Diseases

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    Lozano-Fuentes, S., Bandyopadhyay, A., Cowell, L. G., Goldfain, A., & Eisen, L. (2013). Ontology for vector surveillance and management. Journal of Medical Entomology, 50(1), 1-14. https://doi.org/10.1603/ME12169