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Motivation: The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner is challenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlled vocabularies named Systems Biology Ontology (SBO). The SBO terms enable modelers to explicitly define and describe model entities, including their roles and characteristics., Results: Here, we present the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks., Availability and Implementation: SBOannotator is freely available from https://github.com/draeger-lab/SBOannotator/., (© The Author(s) 2023. Published by Oxford University Press.)

Abnormally high brain aluminum concentrations have been detected in hemodialysis patients who died of an unexplained encephalopathy. As a result, this study was undertaken to examine whether the ingestion of aluminum produces behavioral aberrations in non-dialysed human subjects and rats with ostensibly normal renal function. Rats were fed AlCl3 by intubation in varying doses, and tests measuring learning ability, visual temporal acuity, motor coordination and activity were administered. It was found that orally ingested aluminum is absorbed by rats and deposited in the brain. High brain aluminum levels are associated with rapid general activity, decreased ability to maintain roto-rod activity, and increased sensitivity to flicker. Behavioral tests were also given to elderly human subjects and performance correlated with serum aluminum level. High serum levels of aluminum in elderly humans are associated with impaired visuo-motor coordination, poor long-term memory, and increased sensitivity to flicker.