Abstract
BackgroundBiobanking 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.MethodsBased 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.ResultsBased 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.ConclusionsSharing development principles and Upper Ontologies facilitates subsequent merging of ontologies to achieve a broader coverage.
Highlights
Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing
Ontologized MIABIS (OMIABIS) and Biobank ontology (BO) re-use numerous terms from existing ontologies. Both ontologies were developed based on a methodology that focuses on representation of the real-world phenomena that are described by the data, which is intended to be managed, instead of creating web ontology language (OWL) representations of existing data schemata
We found a few BO terms related to informed consent that overlapped with terms from the Informed Consent Ontology (ICO) [17]
Summary
OBIB is the result of merging two pre-existing ontologies, OMIABIS and BO. we describe criteria and methodologies used by both the developers of OMIABIS and BO. We will give a brief overview over the two source ontologies and describe the merging process in detail Both ontologies, OMIABIS and BO are built based on the principles of the Open Biological and Biomedical Ontologies (OBO) Foundry (http://obofoundry.github.io/ principles/fp-000-summary.html) [10]. 50 terms were added to address biobank specific needs (e.g., collection packets for specimens) resulting in 227 classes, 18 individuals, 34 object properties, and 526 logical axioms. ExternalByhand.owl: terms defined in external OBO Foundry ontologies added manually These files are available on the OMIABIS project website: OMIABIS: https://github.com/OMIABIS/omiabis-dev/ tree/master/BFO2%20omiabis and BO: https://github. These have both been mapped to BFO 2.0 classes, zero-dimensional temporal region and onedimensional temporal region, which were used to replace ConnectedTemporalRegion These merged OWL files are available on github: https://github.com/OMIABIS/omiabis-dev/tree/master/ biobank-omiabis. The consistency of the merged ontology was checked using Hermit 1.3.4 and no inconsistencies were found
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