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An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.

ABSTRACT: BACKGROUND:Dictyostelium discoideum is a model system for studying many important physiological processes including chemotaxis, phagocytosis, and signal transduction. The recent sequencing of the genome has revealed the presence of over 12,500 protein-coding genes. The model organism database dictyBase hosts the genome sequence as well as a large amount of manually curated information. RESULTS:We present here an anatomy ontology for Dictyostelium based upon the life cycle of the organism. CONCLUSION:Anatomy ontologies are necessary to annotate species-specific events such as phenotypes, and the Dictyostelium anatomy ontology provides an essential tool for curation of the Dictyostelium genome.

SUBMITTER: Gaudet P

PROVIDER: S-EPMC2323390 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature

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An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.

Gaudet Pascale P Williams Jeffery G JG Fey Petra P Chisholm Rex L RL

BMC genomics 20080318

<h4>Background</h4>Dictyostelium discoideum is a model system for studying many important physiological processes including chemotaxis, phagocytosis, and signal transduction. The recent sequencing of the genome has revealed the presence of over 12,500 protein-coding genes. The model organism database dictyBase hosts the genome sequence as well as a large amount of manually curated information.<h4>Results</h4>We present here an anatomy ontology for Dictyostelium based upon the life cycle of the o ...[more]

PMID: 18366659

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Project description:Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system's constituents (biological variability). This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation) so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand, and the internal parameters of the single cells on the other.

Dataset Information

An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.

Publications

An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.

Similar Datasets

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