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Ontology Engineering for Biological Applications
2007Ontology engineering is one of the basic components of Semantic Web technology, Ontology engineering provides semantic clarity, explicitness, and facilitates the reusability of represented information and knowledge. We explain the major components of typical ontologies, and the principles behind and different approaches to ontology design.
Larisa N. Soldatova, Ross D. King
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Towards the ontological foundations of symbolic biological theories
Artificial Intelligence in Medicine, 2007Support for the symbolic representation of the physical structure of living organisms by an ontologically solid and logically sound foundation as a basis for formal reasoning.A set of canonical relations and attributes necessary for empirically adequate descriptions of biological entities is proposed.It is shown how a broad range of biological ...
Schulz, Stefan, Hahn, Udo
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Detecting inconsistency in biological molecular databases using ontologies
Data Mining and Knowledge Discovery, 2007The rapid growth of life science databases demands the fusion of knowledge from heterogeneous databases to answer complex biological questions. The discrepancies in nomenclature, various schemas and incompatible formats of biological databases, however, result in a significant lack of interoperability among databases.
Chen, Qingfeng. +2 more
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Using the gene ontology to enrich biological pathways
International Journal of Computational Biology and Drug Design, 2009Most current approaches to automatic pathway generation are based on a reverse engineering approach in which pathway plausibility is solely derived from gene expression data and not independently validated. Alternative approaches use prior biological knowledge to validate automatically inferred pathways, but the prior knowledge is usually not ...
Antonio, Sanfilippo +6 more
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Ontology annotation: mapping genomic regions to biological function
Current Opinion in Chemical Biology, 2007With numerous whole genomes now in hand, and experimental data about genes and biological pathways on the increase, a systems approach to biological research is becoming essential. Ontologies provide a formal representation of knowledge that is amenable to computational as well as human analysis, an obvious underpinning of systems biology.
Paul D, Thomas +2 more
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DEVELOPING ONTOLOGIES IN THE BIOLOGICAL DOMAIN
2023The development of " omic" technologies and its applications into biological sciences has increased the need for an integrated view of bio-related information. The flood of information as well as the technological availability has made it necessary for researchers to share resources and join efforts more than ever in order to understand the ...
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Mereology, Set Theory, Biological Ontology
1994Since 1974, date of publication of M. Ghiselin’s paper “A radical solution to the species problem”, a vigorous polemic has been raging among philosophers of biology on the question of whether biological taxa, and specially biospecies, are classes or individuals.
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Integrating biological pathways in disease ontologies.
Studies in health technology and informatics, 2007Anatomy, clinical features, etiology, and morphology are the major organizing principles in existing disease ontologies. Assuming that biological pathways (including protein physical interactions, metabolic reactions, regulatory networks) will be in the near future key components in classifications of diseases, we have analyzed how information about ...
Julie, Chabalier +2 more
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Biological and Medical Ontologies: Disease Ontology (DO)
Ruba Al Khalaf +2 moreopenaire +1 more source