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Mental exclusions are conceptual representations that relate to the appearances or representations of entities, as discussed by Dignāga.
We also use InChI identifiers as representations of entities stored in databases for which this interpretation is not natural.
Ontologies can be defined as "collections of formal, machine-processable and human-interpretable representations of entities, and the relations between those entities" [ 15].
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The EHCPR specification is quite close to the representation of entities in the real world.
It is a knowledge representation structure, which models a specific domain of interest by providing a formal machine readable representation of entities in the domain.
It allowed the representation of entities such as molecules, atoms, and bonds in our program and the use of functions like removing hydrogen atoms, checking the saturation of a molecule, removing a bond, and many more.
Our team included two post-docs and a data curator with expert understanding of the taxa in the literature under curation, which ensured the accurate representation of entities and phenotypes.
Other distinctive features of NaviCell, compared to CellPublisher, are using markers for selecting entities on the map, decomposing the map into interconnected modules, systematic representation of entities' modifications and their roles in reactions, and a possibility to discuss each object on the map separately.
As usual two stages are involved: first the domain of discourse is enriched with suitable representations of the entities concerned, after which properties over them can be dealt with within the system itself.
Although some chemists thought structural formulas could be understood on a macroscopic basis, others sought to interpret them as representations of microscopic entities called molecules, corresponding to the smallest unit of a compound as an atom was held to be the smallest unit of an element.
As a result of symbols being graphical representations of spatial entities, the automatic conversion of symbols between different standards can be realised, as long as the corresponding symbol codes (names) of the same spatial entity in different mapping standards are clear (Stefanakis 2002; Schlichtmann 2004).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com