Malaria study data integration and information retrieval based on OBO Foundry ontologies

Jie Zheng, Ja Shon Cade, Brian Brunk, David S. Roos, Christian J. Stoeckert, Steven A. Sullivan, Jane M. Carlton, San Emmanuel James, Emmanuel Arinaitwe, Gabriel Carrasco-Escobar, Dionicia Gamboa, Bryan Greenhouse, Grant Dorsey, Paula Maguina-Mercedes, Joseph M. Vinetz

Research output: Contribution to journalArticle

Abstract

The International Centers of Excellence in Malaria Research (ICEMR) projects involve studies to understand the epidemiology and transmission patterns of malaria in different geographic regions. Two major challenges of integrating data across these projects are: (1) standardization of highly heterogeneous epidemiologic data collected by various ICEMR projects; (2) provision of user-friendly search strategies to identify and retrieve information of interest from the very complex ICEMR data. We pursued an ontology-based strategy to address these challenges. We utilized and contributed to the Open Biological and Biomedical Ontologies to generate a consistent semantic representation of three different ICEMR data dictionaries that included ontology term mappings to data fields and allowed values. This semantic representation of ICEMR data served to guide data loading into a relational database and presentation of the data on web pages in the form of search filters that reveal relationships specified in the ontology and the structure of the underlying data. This effort resulted in the ability to use a common logic for storing and display of data on study participants, their clinical visits, and epidemiological information on their living conditions (dwelling) and geographic location. Users of the Plasmodium Genomics Resource, PlasmoDB, accessing the ICEMR data will be able to search for participants based on environmental factors such as type of dwelling, location or mosquito biting rate, characteristics such as age at enrollment, relevant genotypes or gender and visit data such as laboratory findings, diagnoses, malaria medications, symptoms, and other factors.

Original languageEnglish (US)
JournalCEUR Workshop Proceedings
Volume1747
StatePublished - 2016

Fingerprint

Data integration
Foundries
Information retrieval
Ontology
Semantics
Epidemiology
Standardization
Websites
Display devices

Keywords

  • ICEMR
  • OBO Foundry
  • PlasmoDB
  • Standardizing data dictionaries

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Zheng, J., Cade, J. S., Brunk, B., Roos, D. S., Stoeckert, C. J., Sullivan, S. A., ... Vinetz, J. M. (2016). Malaria study data integration and information retrieval based on OBO Foundry ontologies. CEUR Workshop Proceedings, 1747.

Malaria study data integration and information retrieval based on OBO Foundry ontologies. / Zheng, Jie; Cade, Ja Shon; Brunk, Brian; Roos, David S.; Stoeckert, Christian J.; Sullivan, Steven A.; Carlton, Jane M.; James, San Emmanuel; Arinaitwe, Emmanuel; Carrasco-Escobar, Gabriel; Gamboa, Dionicia; Greenhouse, Bryan; Dorsey, Grant; Maguina-Mercedes, Paula; Vinetz, Joseph M.

In: CEUR Workshop Proceedings, Vol. 1747, 2016.

Research output: Contribution to journalArticle

Zheng, J, Cade, JS, Brunk, B, Roos, DS, Stoeckert, CJ, Sullivan, SA, Carlton, JM, James, SE, Arinaitwe, E, Carrasco-Escobar, G, Gamboa, D, Greenhouse, B, Dorsey, G, Maguina-Mercedes, P & Vinetz, JM 2016, 'Malaria study data integration and information retrieval based on OBO Foundry ontologies', CEUR Workshop Proceedings, vol. 1747.
Zheng J, Cade JS, Brunk B, Roos DS, Stoeckert CJ, Sullivan SA et al. Malaria study data integration and information retrieval based on OBO Foundry ontologies. CEUR Workshop Proceedings. 2016;1747.
Zheng, Jie ; Cade, Ja Shon ; Brunk, Brian ; Roos, David S. ; Stoeckert, Christian J. ; Sullivan, Steven A. ; Carlton, Jane M. ; James, San Emmanuel ; Arinaitwe, Emmanuel ; Carrasco-Escobar, Gabriel ; Gamboa, Dionicia ; Greenhouse, Bryan ; Dorsey, Grant ; Maguina-Mercedes, Paula ; Vinetz, Joseph M. / Malaria study data integration and information retrieval based on OBO Foundry ontologies. In: CEUR Workshop Proceedings. 2016 ; Vol. 1747.
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