Biochemistry Procedure-oriented Ontology: A Case Study

Mohammed Alliheedi, Yetian Wang, Robert E. Mercer

2019

Abstract

Ontologies must provide the entities, concepts, and relations required by the domain being represented. The domain of interest in this paper is the biochemistry experimental procedure. The ontology language being used is OWL-DL. OWL-DL was adopted due to its well-balanced flexibility among expressiveness (e.g., class description, cardinality restriction, etc.), completeness, and decidability. These procedures are composed of procedure steps which can be represented as sequences. Sequences are composed of totally ordered, partially ordered, and alternative subsequences. Subsequences can be represented with two relations, directlyFollows and directlyPrecedes that are used to represent sequences. Alternative subsequences can be generated by composing a oneOf function in OWL-DL, referred to it as optionalStepOf in this work, which is a simple generalization of exclusiveOR. Alkaline Agarose Gel Electrophoresis, a biochemistry procedure, is described and examples of these subsequences are provided.

Paper Citation

in Harvard Style

Alliheedi M., Wang Y. and Mercer R. (2019). Biochemistry Procedure-oriented Ontology: A Case Study. In Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K 2019) - Volume 2: KEOD; ISBN 978-989-758-382-7, SciTePress, pages 164-173. DOI: 10.5220/0008167101640173

in Bibtex Style

@conference{keod19,
author={Mohammed Alliheedi and Yetian Wang and Robert E. Mercer},
title={Biochemistry Procedure-oriented Ontology: A Case Study},
booktitle={Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K 2019) - Volume 2: KEOD},
year={2019},
pages={164-173},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008167101640173},
isbn={978-989-758-382-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 11th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K 2019) - Volume 2: KEOD
TI - Biochemistry Procedure-oriented Ontology: A Case Study
SN - 978-989-758-382-7
AU - Alliheedi M.
AU - Wang Y.
AU - Mercer R.
PY - 2019
SP - 164
EP - 173
DO - 10.5220/0008167101640173
PB - SciTePress