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J Biomed Semantics. 2016 May 2;7:23. doi: 10.1186/s13326-016-0068-y. eCollection 2016.

OBIB-a novel ontology for biobanking.

Author information

1
Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., #782, Little Rock, AR 72205-7199 USA.
2
Department of Genetics, Institute for Translational Medicine and Therapeutics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
3
Penn Medicine BioBank, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
4
Department of Biostatistics and Bioinformatics, Duke Medical Center, Duke University, Durnham, USA.
5
Duke Biobank, Duke Translational Research Institute, Duke University, Durnham, USA.

Abstract

BACKGROUND:

Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of biobank-related data. Hitherto no ontology provided the coverage needed to capture a broad spectrum of biobank user scenarios.

METHODS:

Based in the principles laid out by the Open Biological and Biomedical Ontologies Foundry two biobanking ontologies have been developed. These two ontologies were merged using a modular approach consistent with the initial development principles. The merging was facilitated by the fact that both ontologies use the same Upper Ontology and re-use classes from a similar set of pre-existing ontologies.

RESULTS:

Based on the two previous ontologies the Ontology for Biobanking (http://purl.obolibrary.org/obo/obib.owl) was created. Due to the fact that there was no overlap between the two source ontologies the coverage of the resulting ontology is significantly larger than of the two source ontologies. The ontology is successfully used in managing biobank information of the Penn Medicine BioBank.

CONCLUSIONS:

Sharing development principles and Upper Ontologies facilitates subsequent merging of ontologies to achieve a broader coverage.

KEYWORDS:

Biobanking; Biorepository; Ontologies; Terminology

PMID:
27148435
PMCID:
PMC4855778
DOI:
10.1186/s13326-016-0068-y
[Indexed for MEDLINE]
Free PMC Article

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