The Basic-Systems Model of Episodic Memory.

Behavior, neuropsychology, and neuroimaging suggest that episodic memories are constructed from interactions among the following basic systems: vision, audition, olfaction, other senses, spatial imagery, language, emotion, narrative, motor output, explicit memory, and search and retrieval. Each system has its own well-documented functions, neural substrates, processes, structures, and kinds of schemata. However, the systems have not been considered as interacting components of episodic memory, as is proposed here. Autobiographical memory and oral traditions are used to demonstrate the usefulness of the basic-systems model in accounting for existing data and predicting novel findings, and to argue that the model, or one similar to it, is the only way to understand episodic memory for complex stimuli routinely encountered outside the laboratory.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.