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Design of a Biochemistry Procedure-Oriented Ontology

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Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K 2019)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1297))

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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. These procedures are composed of procedure steps which can be represented as sequences. Sequences are composed of totally ordered, partially ordered, and alternative subsequences. 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. In the biochemistry procedure-oriented ontology presented here, subsequences are 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. Each alternative subsequence is referred to as optionalStepOf in this work. Two biochemistry procedures, Alkaline Agarose Gel Electrophoresis and Southern Blotting, are used to demonstrate the generality of this procedural ontology. Portions of these procedures are described in detail. SPARQL queries show the versatility of the ontology.

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Notes

  1. 1.

    http://www.obofoundry.org/ontology/ro.html.

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Author information

Authors and Affiliations

  1. Al Baha University, Al Bahah, 65527, Saudi Arabia

    Mohammed Alliheedi

  2. University of Waterloo, Waterloo, Canada

    Yetian Wang & Robert E. Mercer

  3. The University of Western Ontario, London, Canada

    Robert E. Mercer

Authors
  1. Mohammed Alliheedi
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  2. Yetian Wang
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  3. Robert E. Mercer
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Corresponding author

Correspondence to Mohammed Alliheedi .

Editor information

Editors and Affiliations

  1. Instituto de Telecomunicações, Lisbon, Portugal

    Ana Fred

  2. Federal University of Pernambuco, Recife, Brazil

    Ana Salgado

  3. University of Madeira, Funchal, Portugal

    David Aveiro

  4. Delft University of Technology, Delft, The Netherlands

    Jan Dietz

  5. Polytechnic Institute of Coimbra, Coimbra, Portugal

    Jorge Bernardino

  6. Polytechnic Institute of Setúbal, Setúbal, Portugal

    Joaquim Filipe

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Alliheedi, M., Wang, Y., Mercer, R.E. (2020). Design of a Biochemistry Procedure-Oriented Ontology. In: Fred, A., Salgado, A., Aveiro, D., Dietz, J., Bernardino, J., Filipe, J. (eds) Knowledge Discovery, Knowledge Engineering and Knowledge Management. IC3K 2019. Communications in Computer and Information Science, vol 1297. Springer, Cham. https://doi.org/10.1007/978-3-030-66196-0_17

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  • DOI: https://doi.org/10.1007/978-3-030-66196-0_17

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-66195-3

  • Online ISBN: 978-3-030-66196-0

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