PubMed · 14375969
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G ROMHANYI. 1954. [The relations between structure and function].. https://pubmed.ncbi.nlm.nih.gov/14375969/
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Building an ontology of a defined knowledge domain can help to model an appropriate database structure for the relevant contents. On the other hand, having a comprehensive overview of the knowledge of a certain domain as it may be provided by corresponding databases facilitates building an appropriate ontology, or ontologies with different granularities, which may then provide many additional benefits in handling the stored and in retrieving additional information from heterogenous sources. In this communication, the first steps are reported how we may derive an ontology for the domain of "molecular regulation" from our databases TRANSFAC (transcriptional regulation), TRANSPATH (signal transduction) and CYTOMER (cellular locations).
Although databases for cell signaling pathways include numbers of reaction data of the pathways, the reaction data cannot be used yet to deduce biological functions from them. For the deduction, we need systematic and consistent interpretation of biological functions of reactions in cell signaling pathways in the context of "information transmission". To address this issue, we have developed a functional ontology for cell signaling pathways, Cell Signaling Network Ontology (CSN-Ontology), which provides framework for the functional interpretation presenting some important concepts as information, selectivity, movability, and signaling rules including passage of time.
The concept of a minimal cell is discussed from the viewpoint of comparative genomics. Analysis of published DNA content values determined for 641 different archaeal and bacterial species by pulsed field gel electrophoresis has lead to a more precise definition of the genome size ranges of free-living and host-associated organisms. DNA content is not an indicator of phylogenetic position. However, the smallest genomes in our sample do not have a random distribution in rRNA-based evolutionary trees, and are found mostly in (a) the basal branches of the tree where thermophiles are located; and (b) in late clades, such as those of Gram positive bacteria. While the smallest-known genome size for an endosymbiont is only 450 kb, no free-living prokaryote has been described to have genomes < 1450 kb. Estimates of the size of minimal gene complement can provide important insights in the primary biological functions required for a sustainable, reproducing cell nowadays and throughout evolutionary times, but definitions of the minimum cell is dependent on specific environments.