Modularisation of domain ontologies implemented in description logics and related formalisms including OWL

Rector, Alan L.

doi:10.1145/945649.945664

Cited by 60 publications

(74 citation statements)

References 8 publications

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“…Inspired in part by (Rector, 2003), we advocate the following: Principle of asserted single inheritance. Each reference ontology module should be built as an asserted monohierarchy (a hierarchy in which each term has at most one parent).…”

Section: The Methodology Of Ontological Realismmentioning

confidence: 99%

Ontological realism: A methodology for coordinated evolution of scientific ontologies

Smith¹,

Ceusters²

2010

Applied Ontology

200

119

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Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.

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Section: The Methodology Of Ontological Realismmentioning

confidence: 99%

Ontological realism: A methodology for coordinated evolution of scientific ontologies

Smith¹,

Ceusters²

2010

Applied Ontology

200

119

View full text Add to dashboard Cite

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“…That a more careful use of OWL's disjoint axiom be used throughout the ontology. The BioPAX ontology has the basis for a well structured ontology based on trees of primitive classes [44]. Along with the other recommendations given here, a combination of pulling apart conflated notions and systematic use of disjunction would give a solid foundation for querying BioPAX data.…”

Section: Discussionmentioning

confidence: 99%

e-Science and biological pathway semantics

Luciano

Stevens

2007

BMC Bioinformatics

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Background: The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are placed on the high-throughput data generated and used in these processes. Nowhere is the demand greater than in the semantic integration of these data. Semantic Web tools and technologies afford the chance to achieve this semantic integration. Since pathway knowledge is central to much of the scientific research today it is a good test-bed for semantic integration. Within the context of biological pathways, the BioPAX initiative, part of a broader movement towards the standardization and integration of life science databases, forms a necessary prerequisite for its successful application of e-Science in health care and life science research. This paper examines whether BioPAX, an effort to overcome the barrier of disparate and heterogeneous pathway data sources, addresses the needs of e-Science.

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“…This principle offers the advantages of making the ontology easily extensible and interoperable with other ontologies that have a formal structure. This single-parent structure also helps to build the ontology in a modular fashion whereby different parts of the ontology can be worked on independently [32]. …”

Section: Methodsmentioning

confidence: 99%

NanoParticle Ontology for cancer nanotechnology research

Thomas

Pappu

Baker

2011

Journal of Biomedical Informatics

105

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Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO.

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Modularisation of domain ontologies implemented in description logics and related formalisms including OWL

Cited by 60 publications

References 8 publications

Ontological realism: A methodology for coordinated evolution of scientific ontologies

Ontological realism: A methodology for coordinated evolution of scientific ontologies

e-Science and biological pathway semantics

NanoParticle Ontology for cancer nanotechnology research

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