3,608 research outputs found
Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
As ontologies are developed there is a common need to transform them, especially from those that are axiomatically lean to those that are axiomatically rich. Such transformations often require large numbers of axioms to be generated that affect many different parts of the ontology. This paper describes the Ontology Pre-Processor Language (OPPL), a domain-specific macro language, based in the Manchester OWL Syntax, for manipulating ontologies written in OWL. OPPL instructions can add/remove entities, and add/remove axioms (semantics or annotations) to/from entities in an OWL ontology. OPPL is suitable for applying the same change to different ontologies or at different development stages, and for keeping track of the changes made (e.g. in pipelines). It is also suitable for defining independent modelling macros (e.g. Ontology Design Patterns) that can be applied at will and systematically across an ontology. The presented OPPL Instruction Manager is a Java library that processes OPPL instructions making the changes to an OWL ontology. A reference implementation that uses the OPPL Instruction Manager is also presented. The use of OPPL has been demonstrated in the Cell Cycle Ontolog
OntoQuery: easy-to-use web-based OWL querying
Summary: The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The ProtĆ©gĆ©-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the ProtĆ©gĆ© Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility. Availability and implementation:āThe source code for this implementation together with instructions for installation is available at http://github.com/IlincaTudose/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. Contact: [email protected]
Using Insights from Psychology and Language to Improve How People Reason with Description Logics
Inspired by insights from theories of human reasoning and language, we propose additions to the Manchester OWL Syntax to improve comprehensibility. These additions cover: functional and inverse functional properties, negated conjunction, the definition of exceptions, and existential and universal restrictions. By means of an empirical study, we demonstrate the effectiveness of a number of these additions, in particular: the use of solely to clarify the uniqueness of the object in a functional property; the replacement of and with intersection in conjunction, which was particularly beneficial in negated conjunction; the use of except as a substitute for and not; and the replacement of some with including and only with noneOrOnly, which helped in certain situations to clarify the nature of these restrictions
Populous: A tool for populating ontology templates
We present Populous, a tool for gathering content with which to populate an
ontology. Domain experts need to add content, that is often repetitive in its
form, but without having to tackle the underlying ontological representation.
Populous presents users with a table based form in which columns are
constrained to take values from particular ontologies; the user can select a
concept from an ontology via its meaningful label to give a value for a given
entity attribute. Populated tables are mapped to patterns that can then be used
to automatically generate the ontology's content. Populous's contribution is in
the knowledge gathering stage of ontology development. It separates knowledge
gathering from the conceptualisation and also separates the user from the
standard ontology authoring environments. As a result, Populous can allow
knowledge to be gathered in a straight-forward manner that can then be used to
do mass production of ontology content.Comment: in Adrian Paschke, Albert Burger begin_of_the_skype_highlighting
end_of_the_skype_highlighting, Andrea Splendiani, M. Scott Marshall, Paolo
Romano: Proceedings of the 3rd International Workshop on Semantic Web
Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10,
201
The Distributed Ontology Language (DOL): Use Cases, Syntax, and Extensibility
The Distributed Ontology Language (DOL) is currently being standardized
within the OntoIOp (Ontology Integration and Interoperability) activity of
ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies
formalized in heterogeneous logics, (2) modular ontologies, (3) links between
ontologies, and (4) annotation of ontologies. This paper presents the current
state of DOL's standardization. It focuses on use cases where distributed
ontologies enable interoperability and reusability. We demonstrate relevant
features of the DOL syntax and semantics and explain how these integrate into
existing knowledge engineering environments.Comment: Terminology and Knowledge Engineering Conference (TKE) 2012-06-20 to
2012-06-21 Madrid, Spai
Facets, Tiers and Gems: Ontology Patterns for Hypernormalisation
There are many methodologies and techniques for easing the task of ontology
building. Here we describe the intersection of two of these: ontology
normalisation and fully programmatic ontology development. The first of these
describes a standardized organisation for an ontology, with singly inherited
self-standing entities, and a number of small taxonomies of refining entities.
The former are described and defined in terms of the latter and used to manage
the polyhierarchy of the self-standing entities. Fully programmatic development
is a technique where an ontology is developed using a domain-specific language
within a programming language, meaning that as well defining ontological
entities, it is possible to add arbitrary patterns or new syntax within the
same environment. We describe how new patterns can be used to enable a new
style of ontology development that we call hypernormalisation
Drawing OWL 2 ontologies with Eddy the editor
In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments.
This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification
GO faster ChEBI with Reasonable Biochemistry
Chemical Entities of Biological Interest (ChEBI) is a database and ontology that represents biochemical knowledge about small molecules. Recent changes to the ontology have created new opportunities for automated reasoning with description logic, that have not previously been fully exploited in Chemistry. These changes open up the possibility of building an improved chemical semantic web, by making more use of necessary and sufficient conditions, allowing reasoning about chemical structure, highlighting ambiguous inconsistencies and improving alignment with the Gene Ontology (GO). This paper briefly discusses some of the problems with reasoning over the current version of ChEBI, to tackle these issues, and their potential solutions
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