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  Section: General Botany / Plant Taxonomy
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Taxonomy is the practice and science of classification. The word comes from the Greek τάξις, taxis (meaning 'order', 'arrangement') and νόμος, nomos ('law' or 'science').

Taxonomies, or taxonomic schemes, are composed of taxonomic units known as taxa (singular taxon), or kinds of things that are arranged frequently in a hierarchical structure. Typically they are related by subtype-supertype relationships, also called parent-child relationships. In such a subtype-supertype relationship the subtype kind of thing has by definition the same constraints as the supertype kind of thing plus one or more additional constraints. For example, car is a subtype of vehicle. So any car is also a vehicle, but not every vehicle is a car. Therefore, a thing needs to satisfy more constraints to be a car than to be a vehicle.

Originally the term taxonomy referred to the classifying of living organisms (now known as alpha taxonomy); however, the term is now applied in a wider, more general sense and now may refer to a classification of things, as well as to the principles underlying such a classification.

Almost anything — animate objects, inanimate objects, places, concepts, events, properties, and relationships — may be classified according to some taxonomic scheme. Wikipedia categories illustrate a taxonomy schema.

The term taxonomy may also apply to relationship schemes other than parent-child hierarchies, such as network structures with other types of relationships. Taxonomies may include single children with multi-parents, for example, "Car" might appear with both parents "Vehicle" and "Steel Mechanisms"; to some however, this merely means that 'car' is a part of several different taxonomies.

A taxonomy might also be a simple organization of kinds of things into groups, or even an alphabetical list. However, the term vocabulary is more appropriate for such a list. In current usage within "Knowledge Management", taxonomies are seen as less broad than ontologies as ontologies apply a larger variety of relation types.

Mathematically, a hierarchical taxonomy is a tree structure of classifications for a given set of objects. It is also named Containment hierarchy. At the top of this structure is a single classification, the root node, that applies to all objects. Nodes below this root are more specific classifications that apply to subsets of the total set of classified objects. So for instance, in common schemes of scientific classification of organisms, the root is called "Organism" followed by nodes for the taxonomic ranks: Domain, kingdom, phylum, class, etc. The progress of reasoning proceeds from the general to the more specific. In scientific taxonomies, a conflative term is always a polyseme.

In contrast, in a context of legal terminology, an open-ended contextual taxonomy -- a taxonomy holding only with respect to a specific context. In scenarios taken from the legal domain, a formal account of the open-texture of legal terms is modeled, which suggests varying notions of the "core" and "penumbra" of the meanings of a concept. The progress of reasoning proceeds form the specific to the more general.

Taxonomy and mental classification
Some have argued that the adult human mind naturally organizes its knowledge of the world into such systems. This view is often based on the epistemology of Immanuel Kant. Anthropologists have observed that taxonomies are generally embedded in local cultural and social systems, and serve various social functions. Perhaps the most well-known and influential study of folk taxonomies is Émile Durkheim's The Elementary Forms of Religious Life.

Various taxonomies
Linnaean taxonomy is the system most familiar to non-taxonomists. It uses the formal taxonomic ranks (in order) Kingdom, Phylum, Class, Order, Family, Genus, Species. The lower ranks (superfamily to subspecies) are strictly regulated, e.g. by the ICZN for animals, whereas taxonomy at higher ranks is a result of consensus in the scientific community. How researchers arrive at their taxa varies; depending on the available data and resources; methods vary from simple qualitative comparisons for little-documented organisms to elaborate cladistic analyses for well-known groups with abundant DNA sequence data. (Various mnemonic devices have been used to help people remember the list of Linnaean taxonomic ranks.)

In phylogenetic taxonomy, cladistic taxonomy or cladism, organisms are classified into "clades", which are discovered by grouping taxa using derived traits. By using clades as the criteria for separation, cladistic taxonomy, using cladograms, can categorize taxa into unranked groups. The taxonomy is exclusively based on cladistic analysis.

In numerical taxonomy, phenetics or taximetrics, the taxonomy is exclusively based on cluster analysis and neighbor joining to best-fit numerical equations that characterize all measurable quantities of a number of organisms. This method has been largely superseded by the superior cladistic analyses today, except in cases when these are too computationally intensive (a single large-scale cladistic analysis can take months to compute).

Non-scientific taxonomies
Other taxonomies, such as those analyzed by Durkheim and Lévi-Strauss, are sometimes called folk taxonomies to distinguish them from scientific taxonomies that focus on evolutionary relationships rather than similarity in habitus and habits. Though phenetics arguably places much emphasis on overall similarity, it is a quantitative analysis that attempts to reproduce evolutionary relationships of lineages and not similarities of form taxa.

The neologism folksonomy should not be confused with "folk taxonomy", though it is obviously a portmanteau created from the two words. "Fauxonomy" (from French faux, "false") is a pejorative neologism used to criticize folk taxonomies for their lack of agreement with scientific findings. Baraminology is a taxonomy used in creation science which in classifying form taxa resembles folk taxonomies.

The phrase "enterprise taxonomy" is used in business to describe a very limited form of taxonomy used only within one organization. An example would be a certain method of classifying trees as "Type A", "Type B" and "Type C" used only by a certain lumber company for categorising log shipments.

Military taxonomy
Military theorist Carl von Clausewitz stressed the significance of grasping the fundamentals of any situation in the "blink of an eye" (coup d'œil). In a military context, the astute tactician can immediately grasp a range of implications and can begin to anticipate plausible and appropriate courses of action. Clauzewitz' conceptual "blink" represents a tentative ontology which organizes a set of concepts within a domain.

The term "military taxonomy" encompasses the domains of weapons, equipment, organizations, strategies, and tactics. The use of taxonomies in the military extends beyond its value as an indexing tool or record-keeping template -- for example, the taxonomy-model analysis suggests a useful depiction of the spectrum of the use of military force in a political context.

A taxonomy of terms to describe various types of military operations is fundamentally affected by the way all elements are defined and addressed -- not unlike framing. For example, in terms of a specific military operation, a taxonomic approach based on differentiation and categorization of the entities participating would produce results which were quite different from an approach based on functional objective of an operation (such as peacekeeping, disaster relief, or counter-terrorism).

- Zirn, C⇒cilia, Vivi Nastase and Michael Strube. "Distinguishing Between Instances and Classes in the Wikipedia Taxonomy"
- Jackson, Joab. "Taxonomy’s not just design, it’s an art," Government Computer News (Washington, D.C.). September 2, 2004.
- Malone, Joseph L. (1988). The Science of Linguistics in the Art of Translation: Some Tools from Linguistics for the Analysis and Practice of Translation, p. 112.
- Grossi, Davide, Frank Dignum and John-Jules Charles Meyer. (2005). "Contextual Taxonomies" in Computational Logic in Multi-Agent Systems, pp. 33-51.
- Fenske, Russell W. "A Taxonomy for Operations Research," Operations Research, Vol. 19, No. 1 (Jan.-Feb., 1971), pp. 224-234; United Nations. "Taxonomy for Recordkeeping in Field Missions of UN Peacekeeping Operations." June 2006.
- Cohen, Stuart A. and Efraim Inbar. "A taxonomy of Israel's use of military force," Journal Comparative Strategy, Vol. 10, No. 2 (April 1991), pp. 121 - 138.
- Downie, Richard D. "Defining integrated operations," Joint Force Quarterly (Washington, D.C.). July, 2005.

- Carbonell, J. G. and J. Siekmann, eds. (2005). Computational Logic in Multi-Agent Systems, Vol. 3487.
- Clausewitz, Carl. (1982). On War (editor, Anatol Rapoport). New York: Penguin Classics.
- Malone, Joseph L. (1988). The Science of Linguistics in the Art of Translation: Some Tools from Linguistics for the Analysis and Practice of Translation. Albany, New York: State University of New York Press.

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