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Biological and Medical Ontologies: Systems Biology Ontology (SBO)
2019The Systems Biology Ontology (SBO) comprises a number of controlled vocabularies containing terms commonly used in Systems Biology, in particular in computational modelling. It is applied, among other ontologies, within the Systems Biology Markup Language (SBML) to restrict and better characterize the components of models.
A. Bernasconi, M. Masseroli
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Biological and Medical Ontologies: Human Phenotype Ontology (HPO)
2019The Human Phenotype Ontology (HPO) consists of a well-defined and comprehensive set of more than 12,000 terms, a standard structured terminology regarding phenotypic abnormalities observed in human disease, and their relationships. The HPO project provides a collection of over 250,000 computational assertions that a disease (rare or common) is ...
A. Bernasconi, M. Masseroli
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Ontology-Based Aggregation of Biological Pathway Datasets
2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, 2005The massive accumulation of biological data in the past decades has generated a significant amount of biological knowledge which is represented in one way as biological pathways. The existence of over 150 pathway databases reflects the diversity of the biological data and heterogeneity of data models, storage formats and access methods.
Keyuan, Jiang, Christopher, Nash
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On the ontology of biological aging
Archives of Gerontology and Geriatrics, 1988The central question in the field of experimental gerontology is: what is biological aging? It is true that a living body must obey the laws of causal determinism; like all bodies it is subject to the physical and chemical laws of the phenomenal world.
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On the Ontology of Biological Species
2018In this paper, two different ontological views concerning biological species are analyzed. On the first view, species are universals instantiated by the members of the species, while, according to the second view, species are complex individuals formed by the members of the species.
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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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