@inbook {26441, title = {Design of a Biochemistry Procedure-Oriented Ontology}, booktitle = {the Communications in Computer and Information Science book series}, volume = {1297}, year = {2020}, pages = {65-387}, publisher = {Springer}, organization = {Springer}, 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.

}, url = {https://doi.org/10.1007/978-3-030-66196-0_17}, author = {Mohammed Alliheedi and Yetian Wang and Robert E. Mercer} }