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Table 2 Definitions of KEfED processes and entities for the tract-tracing experiment workflow

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

Element Definition Ontology term
Experimental Subject The living organism that is the subject of the experiment. obi:OBI_0100026 ('organism')
Injection A microinjection of tracer into the brain of the experimental subject. obi:OBI_0000426 ('injection')
Perfusion Euthanizing, exsanguinating, and then perfusion-fixing the tissue of an experimental animal. In our case, we also include in this step the process of tissue dissection that extracts the brain from the body and preserves it (by freezing) for subsequent histological processing. obi:OBI_0000919 ('animal euthanization')
Brain The post-mortem dissected brain of an experimental subject fma:FMA_50801 ('Brain')
Tissue Sectioning The process of cutting a biological sample (in our case, a dissected brain) into thin tissue sections for histological staining and processing. nif:birnlex_2156 ('Tissue sectioning')
Tissue Sections Unmounted thin sections of tissue (thickness typically less than 100 microns) for subsequent histochemistry, staining and mounting nif:birnlex_2169 ('Tissue section')
Immunohisto-chemistry The process of histochemistry, staining and mounting of tissue sections onto microsope slides. nif:nlx_inv_20090609 ('Immunohistochemistry')
Immunostained Slides Thin sections of tissue that have been mounted on glass slides for subsequent microscopic examination and analysis -
Neuroanatomical mapping and analysis The process of microscopically examining neuroanatomical sections in order to place accurately the location of histological staining into the context of a standard brain atlas/parcellation scheme. obi:OBI_0600020 ('histology')
  1. KEfED model elements for the processes and entities in the tract-tracing experiment, showing the closely matched terms from community-driven ontologies. Those terms were added to the KEfED model elements using the editor's ontology search interface. Sources of the terms are the Ontology of Biomedical Investigation ('obi: 'http://purl.obolibrary.org/obo/, [44]), the Foundational Model of Anatomy ('fma: 'http://purl.org/obo/owl/FMA#, [73]), the Neuroscience Information Framework ('nif: 'http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#, [74]). The matched term is intended to be as close a semantic match as possible. If a specialized term is not available, a more general encompassing term is used.