The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

Journal of Biomedical Semantics 7 (53) (2016)
  Copy   BIBTEX

Abstract

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research.

Other Versions

No versions found

Links

PhilArchive

External links

  • This entry has no external links. Add one.
Setup an account with your affiliations in order to access resources via your University's proxy server

Through your library

Similar books and articles

OBCS: The Ontology of Biological and Clinical Statistics.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith & Yongqun He - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:65.
CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIViewH.Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He & Alpha Tom Kodamullil - 2021 - Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS).
Dealing with elements of medical encounters: An approach based on ontological realism.Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.
A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
The ImmPort Antibody Ontology.William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg & Alexander D. Diehl - 2016 - Proceedings of the International Conference on Biological Ontology 1747.

Analytics

Added to PP
2016-10-08

Downloads
649 (#40,849)

6 months
110 (#53,505)

Historical graph of downloads
How can I increase my downloads?

Author's Profile

Barry Smith
University at Buffalo

Citations of this work

No citations found.

Add more citations

References found in this work

SNAP and SPAN: Towards dynamic spatial ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.

View all 7 references / Add more references