Title: Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformation

Authors: Arash Shaban-Nejad; Volker Haarslev

Addresses: McGill Centre for Clinical and Health Informatics, Department of Epidemiology and Biostatistics, McGill University, 1140 Pine Avenue West, Montreal, Quebec, H3A 1A3, Canada ' Department of Computer Science and Software Engineering, Concordia University, 1455 de Maisonneuve Blvd. W., Montreal, Quebec H3G 1M8, Canada

Abstract: The issue of ontology evolution and change management is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies and interactions with other existing ontologies have been widely neglected. In our research, after revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, Represent, Legitimate and Reproduce (RLR), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general and aids in tracking and representing the changes, particularly through the use of category theory and hierarchical graph transformation.

Keywords: controlled vocabulary; bio-ontologies; hierarchical graph transformation; category theory; ontology change management; ontology evolution; distributed ontologies; biomedical ontologies; bioinformatics; agent-based systems; multi-agent systems; MAS.

DOI: 10.1504/IJDMB.2015.066334

International Journal of Data Mining and Bioinformatics, 2015 Vol.11 No.1, pp.53 - 83

Received: 20 Sep 2012
Accepted: 02 Nov 2012

Published online: 17 Dec 2014 *

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