Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

  • Wheeler D
  • White C
  • Rees C
  • et al.
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Abstract

Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness.The hippocampus is a seahorse-shaped region of the brain that is responsible for learning, emotions, and memory. Like other regions of the brain, it contains many types of neurons that send information to each other by releasing chemicals called neurotransmitters across junctions known as synapses. Identifying all the different neuron types in the hippocampus is an important step towards understanding in detail how this brain region works.Thousands of articles have been published that attempt to characterize the neurons in the hippocampus, but many of these studies report only some of the properties of a new neuron type. It is also often difficult to compare the results of different studies, as many different approaches have been used to investigate neuron types, and different studies often use different terms to describe similar features.Wheeler et al. have now created a resource called Hippocampome.org that combines approximately 14,000 pieces of experimental evidence about neuron types in the rat hippocampus into a unified database. Analyzing these data has revealed about 3700 different neuron properties. By primarily considering the pattern formed by the branched axons and dendrites, the outputs and inputs that extend out of a neuron, Wheeler et al. have identified over a hundred different neuron types. This classification system also considers how selectively the neuron forms synapses with other cells and the identity of the neurotransmitter released by the neuron. In the future, other features of the neurons will also be incorporated into the system to help refine the classifications.All of this information is online and freely available at Hippocampome.org. This resource is expected to provide a solid basis for analyzing how the hippocampus works, by helping researchers to design and interpret experiments and simulations.

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Wheeler, D. W., White, C. M., Rees, C. L., Komendantov, A. O., Hamilton, D. J., & Ascoli, G. A. (2015). Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus. ELife, 4. https://doi.org/10.7554/elife.09960

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