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Table 1 Definitions of KEfED variables for tract-tracing experiments

From: Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case

Variable Definition
Taxonomic class Within this example we adopt the designation of taxonomic Specification from the NCBI's taxonomy database [63].
Injection.chemical The chemical molecule injected into the brain of an animal as part of a tract-tracing experiment. These reagents are not confined to a specific type of chemical simply have the property of when injected into brain tissue, they are taken up and transported along axons by active processes in neurons. Early examples of these include tritiated amino acids [64], Horseradish peroxidase (HRP) [65] and notably Phaseolus Leuco-Agglutinin [66]. Tracer chemicals include fluorescent dyes and beads and even include more exotic materials such as viruses and Cholera Toxin. See [17, 6771] for reviews of the general and specialized methods used.
Injection.location This refers to the extent of the complete injection site expressed in terms of its spatial relationships to identified brain structures from the Swanson atlas [32] and encoded into the neuroanatomical nomenclature specified from the BAMS system [72]
Mapped location Similarly to Injection.location, this refers to the spatial extent of an individual region of labeling (judged by the scientist reporting the study to be relatively homogeneous) expressed in terms of its spatial relationships to named neuroanatomical terms from the BAMS ontology [72]
Labeling.type A simple categorization of the part of the neuron that is labeled. This is a nominal data element with possible values 'cellular' (denoting that the neuronal cell bodies were labeled), ' fibers' (denoting that axonal fibers were labeled), or 'terminals' (denoting that axonal fibers with characteristics of a terminal region were labeled, including heavy branching and the presence of boutons).
Labeling.density A simple, seven point ordinal scale with the following categories (in order): 'no label', 'very sparse label, 'sparse label', 'sparse/moderate label', 'moderate label', 'moderate/dense label' and 'dense label'. We also include an additional category to denote that labeling is present but with an unknown density.
  1. Definitions for the variables used in the tract-tracing study. The KEfED system allows for complex multi-attribute variables (such as Injection.chemical and Injection.location).