Accordingly, the TOL might be understood as a represented entities TOL (a tree-like model that is built from the source entities using various computational tools, some of which might in addition include hierarchical branching assumptions), or as an interpreted entities TOL (an interpretation of the previous tree-like model in terms of organisms or species for instance).
Epistemology refers, in the broadest sense, to the methods that we use to study the world and the perspective that a researcher uses to interpret entities and phenomena.
(2) Given a represented entities TOL (for instance a gene tree), is the interpreted entities TOL (for instance a species tree) true -- in the sense that if the corresponding real entities phylogeny were known, the two would match -- or is it false due to a wrong interpretation?
Instead of interpreting individual entities separately, a priori knowledge about their interactions and common functions can be used to identify modules that are jointly affected by the condition of interest.
Advanced data integration requires the ability to unambiguously interpret conceptual entities such that data may be shared and re-used at any time in the future.
4. It is tempting to assume that familiar biological objects, like "cell" are represented in the model from the structural perspective, i.e. that there is a structural entity interpreted as "cell".
Because an author may define new tags, an XML DTD must also contain rules that instruct a Web browser how to interpret them—how an entity is to be displayed or how it is to generate an action such as preparing an e-mail message.
Second, it requires a shared perspective that allows the organisation to be interpreted as a common entity [21].
This perceptual principle states that a continuous (straight or curved) line is interpreted as a single entity.
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