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|Title: ||The consistent representation of scientific knowledge : investigations into the ontology of karyotypes and mitochondria|
|Authors: ||Warrender, Jennifer Denise|
|Issue Date: ||2015 |
|Publisher: ||Newcastle University|
|Abstract: ||Ontologies are widely used in life sciences to model scienti c knowledge. The engineering
of these ontologies is well-studied and there are a variety of methodologies
and techniques, some of which have been re-purposed from software engineering
methodologies and techniques. However, due to the complex nature of bio-ontologies,
they are not resistant to errors and mistakes. This is especially true for more expressive
and/or larger ontologies.
In order to improve on this issue, we explore a variety of software engineering techniques
that were re-purposed in order to aid ontology engineering. This exploration
is driven by the construction of two light-weight ontologies, The Mitochondrial Disease
Ontology and The Karyotype Ontology. These ontologies have speci c and
useful computational goals, as well as providing exemplars for our methodology.
This thesis discusses the modelling decisions undertaken as well as the overall success
of each ontological model. Due to the added knowledge capture steps required
for the mitochondrial knowledge, The Karyotype Ontology is further developed than
The Mitochondrial Disease Ontology.
Speci cally, this thesis explores the use of a pattern-driven and programmatic approach
to bio-medical ontology engineering. During the engineering of our biomedical
ontologies, we found many of the components of each model were similar
in logical and textual de nitions. This was especially true for The Karyotype Ontology.
In software engineering a common technique to avoid replication is to abstract
through the use of patterns. Therefore we utilised localised patterns to model
these highly repetitive models. There are a variety of possible tools for the encoding
of these patterns, but we found ontology development using Graphical User
Interface (GUI) tools to be time-consuming due to the necessity of manual GUI
interaction when the ontology needed updating. With the development of Tawny-
OWL, a programmatic tool for ontology construction, we are able to overcome this
issue, with the added bene t of using a single syntax to express both simple and
- i -
patternised parts of the ontology.
Lastly, we brie
y discuss how other methodologies and tools from software engineering,
namely unit tests, di ng, version control and Continuous Integration (CI) were
re-purposed and how they aided the engineering of our two domain ontologies.
Together, this knowledge increases our understanding in ontology engineering techniques.
By re-purposing software engineering methodologies, we have aided construction,
quality and maintainability of two novel ontologies, and have demonstrated
their applicability more generally.|
|Description: ||PhD Thesis|
|Appears in Collections:||School of Computing Science|
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