Taxonomy: Wikis

  
  
  

Encyclopedia

From Wikipedia, the free encyclopedia

.Taxonomy is the practice and science of classification.^ In science, taxonomy is the formal classification of organisms.

^ Taxonomy The science dealing with the identification, naming, and classification of plants and animals.
  • USGS Paleontology - Glossary of Terms 21 January 2010 3:27 UTC geology.er.usgs.gov [Source type: FILTERED WITH BAYES]

.The word finds its roots in the Greek τάξις, taxis (meaning 'order', 'arrangement') and νόμος, nomos ('law' or 'science').^ The word Paleozoic is from Greek and means "old life."
  • USGS Paleontology - Glossary of Terms 21 January 2010 3:27 UTC geology.er.usgs.gov [Source type: FILTERED WITH BAYES]

^ [L] “evaluate, estimate, assess, handle” taxi = short for “taximeter”= “charging (assess) meter” [L] taxidermy = “taxis”[Gk] = “arrangement” + dermis [Greek] = “skin” taxonomy = “taxis”[Gk] = “order, arrangement” + “Nomos ” = “law” or “science” ataxia = “a” [Gk] “not” + “taxis”=ordered.

^ The word Mesozoic is from Greek and means "middle life."
  • USGS Paleontology - Glossary of Terms 21 January 2010 3:27 UTC geology.er.usgs.gov [Source type: FILTERED WITH BAYES]

.Taxonomy uses taxonomic units, known as taxa (singular taxon).^ Linnaeus grouped taxa (singular taxon) into hierarchical groups.

^ The Linnaean system breaks down organisms into seven major divisions, called taxa (singular: taxon).
  • Taxonomy 21 January 2010 3:27 UTC www.msu.edu [Source type: FILTERED WITH BAYES]

^ Taxonomy Resources This site provides the list of all the taxonomic resources, including books, articles, and Web sites, used by GenBank's taxonomy group.
  • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

In addition, the word is also used as a count noun: a taxonomy, or taxonomic scheme, is a particular classification ("the taxonomy of ..."), arranged in a hierarchical structure. .Typically this is organized by supertype-subtype relationships, also called generalization-specialization relationships, or less formally, parent-child relationships.^ It uses the special-general "is a kind of" relationship.
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ Typically we draw the most general classes at the top of a diagram and a tree of more specialized classes below them.
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ The relationships generally go beyond the standard BT, NT, and RT. They may include specific whole-part, cause-effect, or parent-child relationships.
  • Taxonomy Glossary 21 January 2010 3:27 UTC www.taxotips.com [Source type: Reference]

.In such an inheritance relationship, the subtype by definition has the same properties, behaviors, and constraints as the supertype plus one or more additional properties, behaviors, or constraints.^ Codominance Also: codominant relationship in which two or more animals are equally positioned in the social dominance hierarchy and have equal priority, access, and superiority in regards to feeding, sexual, and locomotion behavior .
  • Primate Factsheets: Glossary 21 January 2010 3:27 UTC pin.primate.wisc.edu [Source type: FILTERED WITH BAYES]

^ One important task is to identify whether two or more nodes represent the same person.
  • Tasks Taxonomy for Graphs - InfoVis:Wiki 21 January 2010 3:27 UTC www.infovis-wiki.net [Source type: FILTERED WITH BAYES]

^ One or more persons having such ability.
  • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

For example, car is a subtype of vehicle. So any car is also a vehicle, but not every vehicle is a car. .Therefore, a type needs to satisfy more constraints to be a car than to be a vehicle.^ More often than not, your classification requirements will vary by content class or type.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

^ But be prepared to discover that on or more of them is tougher than you thought and may need to be put on a "backlog".
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

Another example, any shirt is also a piece of clothing, but not every piece of clothing is a shirt. .Hence, a type must satisfy more parameters to be a piece of clothing than to be a shirt.^ More often than not, your classification requirements will vary by content class or type.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

Contents

Applications

.Originally taxonomy referred only to the classifying of organisms (now sometimes known as alpha taxonomy) or a particular classification of organisms.^ In science, taxonomy is the formal classification of organisms.

^ The label "Taxonomic organism of test fragment absent from reference set" refers when the test fragment is classified using a reference set not containing the source organism from which the test fragment originates from.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ As expected, having the source organisms of classified fragments included in the reference set has a markedly positive impact on the accuracy at all taxonomic ranks.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

.However, it has become fashionable in certain circles to apply the term in a wider, more general sense, where it may refer to a classification of things or concepts, as well as to the principles underlying such a classification.^ Oh, and resurrect the term and term relationship caches in a more term generic fashion.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ The word "religion" is also used in a generic sense, not applied to a specific belief system or philosophy.
  • Levels of Classification of Faith Groups 25 September 2009 9:32 UTC www.adherents.com [Source type: FILTERED WITH BAYES]

^ MEGAN [ 17 ] performs well in classifying genomic fragments if closely related reference genomes are available, which may not be always the case for organisms contained in an environmental sample.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

.Almost anything—animate objects, inanimate objects, places, concepts, events, properties, and relationships—may then be classified according to some taxonomic scheme.^ Agents may be usefully classified according to the subset of these properties that they enjoy.

^ Test: If A is a superclass of B then every object in class B is automatically also an object of class A. Every property of objects in A is automatically a property of B. Chapter 24 pp 407-411 -- taxonomic classification .
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ Having settled on a much less restrictive definition of an autonomous agent, these properties may help us further classify agents in useful ways.

.Wikipedia categories illustrate a taxonomy schema[1] and a full taxonomy of Wikipedia categories can be extracted by automatic means[2].^ Create a generic taxonomy and term API and schema that can be used for tags, post categories, link categories, and arbitrary future taxonomies.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

.Recently, it has been shown that a manually-constructed taxonomy, such as that of computational lexicons like WordNet, can be used to improve and restructure the Wikipedia category taxonomy[3].^ This function only works for hierarchical taxonomies like post categories.
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ Create a generic taxonomy and term API and schema that can be used for tags, post categories, link categories, and arbitrary future taxonomies.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ I quite like this anyway, as it also allows for more complicated taxonomy schemes, such as linked lists.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

.In an even wider sense, the term taxonomy could also be applied to relationship schemes other than parent-child hierarchies, such as network structures with other types of relationships.^ If the term is a parent of other terms, then the children will be updated to .
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ The taxonomy which determines the hierarchy of the terms.
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ Will remove the term's relationship to the taxonomy, not the term or taxonomy .
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

Taxonomies may then 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.^ Otherwise how would people in different parts of the world talk about animals and be certain that they both know exactly which animal they are talking about?
  • ACS - American Cetacean Society 21 January 2010 3:27 UTC www.acsonline.org [Source type: FILTERED WITH BAYES]

^ Because computers require data to be both predictable and comprehensive, a taxonomy structure often requires that each term appear in only one place in the hierarchy and that all terms be included.
  • Ten taxonomy myths 21 January 2010 3:27 UTC www.montague.com [Source type: Reference]

^ Redundancy; needless repetition of the same meaning in what are merely different words.
  • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

[4] .A taxonomy might also be a simple organization of kinds of things into groups, or even an alphabetical list.^ "A taxonomy is a system for naming and organizing things into groups that share similar characteristics."
  • Ten taxonomy myths 21 January 2010 3:27 UTC www.montague.com [Source type: Reference]

^ Back to Top The NASA Taxonomy is expressed in an XML language called SKOS which stands for Simple Knowledge Organizing System.

^ Scientific classification is the method scientists have developed to arrange all of the world's organisms both extinct and living things into groups.

.However, the term vocabulary is more appropriate for such a list.^ In many cases, you will see a See Also section with one or more taxonomy codes/terms listed beneath it.
  • Win 2-1-1 - Help - Taxonomy Information - The information on the taxonomy definition page 21 January 2010 3:27 UTC www.resourcehouse.com [Source type: General]

^ I quite like this anyway, as it also allows for more complicated taxonomy schemes, such as linked lists.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ That radical feminism was a term highjacked from feminists with Marxist leanings and appropriated by a more conservative essentialism that privileged personal style over political coalitions.
  • Taxonomy of Feminist Intellectual Traditions 21 January 2010 3:27 UTC home.sou.edu [Source type: FILTERED WITH BAYES]

.In current usage within Knowledge Management, taxonomies are considered narrower than ontologies since ontologies apply a larger variety of relation types.^ If human beings are the primary taxonomy users, integration can be "loose," consisting of web-like structures where links point to a variety of resource types (including people).
  • Ten taxonomy myths 21 January 2010 3:27 UTC www.montague.com [Source type: Reference]

^ One aspect of understanding is the knowledge of how things hang together, and how things within a topic relate to each other.
  • A Taxonomy of WebQuest Tasks 21 January 2010 3:27 UTC webquest.sdsu.edu [Source type: FILTERED WITH BAYES]

^ I figure most of the term manipulation will be done within the context of a taxonomy, so just have add_term() add the term to the terms table and take care of adding the term_taxonomy relation.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

[5]
.Mathematically, a hierarchical taxonomy is a tree structure of classifications for a given set of objects.^ Whether the taxonomy object is hierarchical.
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ Bloom's Taxonomy refers to a classification of the different learning objectives that educators set for students.
  • Documents Tagged with blooms taxonomy | Scribd 21 January 2010 3:27 UTC www.scribd.com [Source type: General]

^ One of the examples of such perfect Taxonomy is structured by Swedish scientist; his biological classification is in use till today.
  • Taxonomy | Moving Clouds 21 January 2010 3:27 UTC brutonbioenergy.com [Source type: FILTERED WITH BAYES]

It is also named Containment hierarchy. .At the top of this structure is a single classification, the root node, that applies to all objects.^ Content classified under nodes within a single set may have relevance because they are related by something inherent in the structure (they’re all part of the same ancestor).
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

^ It can take an array of objects and taxonomies (or singles of each) and does one query to get it all out in one go.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ An enterprise taxonomy is typically perceived as a single, monolithic, corporation-wide, structure for the classification of all things related to your business.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

.Nodes below this root are more specific classifications that apply to subsets of the total set of classified objects.^ The effect of taxonomy classification is to easily and more precisely apply metadata to content so information is more easily found by enterprise search engines.
  • Smartlogic :: Taxonomy Classification / Software, Sharepoint Metadata and Ontology / Semantic Search 21 January 2010 3:27 UTC smartlogic.com [Source type: FILTERED WITH BAYES]

^ This means, more often than not, the scope of your content classification requirements will be constrained to some subset of the organization or to a particular business process.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

^ At each taxonomic rank, the classification accuracy (specificity and sensitivity) achieved for two different intrinsic classifiers: TACOA and PhyloPythia is given.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

The progress of reasoning proceeds from the general to the more specific. In scientific taxonomies, a conflative term is always a polyseme.[6]
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.^ Nanoscale Computation/Modeling Domain Expert Opening at Lurie Nanofabrication Facility .

The progress of reasoning proceeds from the specific to the more general.[7]

Taxonomy and mental classification

.Some have argued that the adult human mind naturally organizes its knowledge of the world into such systems.^ "A taxonomy is a system for naming and organizing things into groups that share similar characteristics."
  • Ten taxonomy myths 21 January 2010 3:27 UTC www.montague.com [Source type: Reference]

^ Some argue there should be a single system of rules for naming all organisms; a draft version of this proposed "Biocode" is provided at this web site.

^ Today, taxonomic systems strive to cluster organisms into natural hierarchical groupings based upon morphology and phylogeny.

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.^ In a human service context, a taxonomy is a classification system that allows you to index and access community resources based on the services they provide and the target populations they serve, if any.
  • MinnesotaHelp.info - Help - Taxonomy Information - What is a taxonomy? 21 January 2010 3:27 UTC minnesotahelp.info [Source type: General]
  • MinnesotaHelp.info - Help - Taxonomy Information 21 January 2010 3:27 UTC www.minnesotahelp.org [Source type: Reference]

^ And a local variable is available for abuse in only a part of a function and so is the safest.
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ The idea of adding various helper functions to do the queries is excellent, as it will save people time and also serve as models for how to do custom queries in plugins for other purposes.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

.Perhaps the most well-known and influential study of folk taxonomies is Émile Durkheim's The Elementary Forms of Religious Life.^ Earth has too much biodiversity and you go back to your home planet, defeated by carbon-based life-form taxonomy.

^ Geology The study of the planet Earth - the materials of which it is made, the processes that act on these materials, the products formed, and the history of the planet and its life forms since its origin [ Top of Page ] .
  • USGS Paleontology - Glossary of Terms 21 January 2010 3:27 UTC geology.er.usgs.gov [Source type: FILTERED WITH BAYES]

A more recent treatment of folk taxonomies (including the results of several decades of empirical research) and the discussion of their relation to the scientific taxonomy can be found in Scott Atran's Cognitive Foundations of Natural History.

Various biological taxonomies

.Biological classification (sometimes known as "Linnaean taxonomy") is still generally the best known form of taxonomy.^ This form of "bookkeeping", known as taxonomy, was started by Swedish physician and naturalist, Carolus Linnaeus (1707-1778), in his work Systema Naturae , in 1735.
  • ACS - American Cetacean Society 21 January 2010 3:27 UTC www.acsonline.org [Source type: FILTERED WITH BAYES]

^ The biological taxonomy takes the form of a tree with "living creatures" at the root and individual species at the leaves.

^ A blog devoted to SharePoint Taxonomy and Governance best practices and just generally doing SharePoint on purpose!
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

.It differs from the above in that it is an empirical science, with classifying only the final step of a process, and a classification only the means to communicate the end results.^ This means, more often than not, the scope of your content classification requirements will be constrained to some subset of the organization or to a particular business process.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

^ At each taxonomic rank, the classification accuracy (specificity and sensitivity) achieved for two different intrinsic classifiers: TACOA and PhyloPythia is given.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ Unsupervised methods are for example employed as a pre-processing step for assembly or to study the community composition of samples.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

It also includes the prediction, discovery, description and (re)defining of taxa. .It uses taxonomic ranks, including, among others, (in order) Kingdom, Phylum, Class, Order, Family, Genus, Species (various mnemonic devices have been used to help people remember the list of "Linnaean" taxonomic ranks.^ I know the kingdom, genus and species.
  • Mushroom Taxonomy (MushroomExpert.Com) 21 January 2010 3:27 UTC www.mushroomexpert.com [Source type: FILTERED WITH BAYES]

^ Class - The taxonomic group below a Phylum, and above Order.
  • http://www.marine-medic.com.au/pages/glossary.asp 21 January 2010 3:27 UTC www.marine-medic.com.au [Source type: FILTERED WITH BAYES]

^ From most specific to most general we have: species, genus, family, order, class, phylum, and kingdom.

See Zoology mnemonic). .In zoology, the nomenclature for the more important ranks (superfamily to subspecies), including the allowed number of ranks, is strictly regulated by the ICZN Code, whereas there is more latitude for names at higher ranks.^ For longer contigs (DNA fragments of length 10 Kbp) PhyloPythia is more sensitive on higher taxonomic ranks (superkingdom, phylum and class).
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ Is it generally worth throwing in more classes for higher cohesion and lower coupling, even if it means the number of classes, and pehaps complexity, goes up?
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ [But] if life continues, and if in continuing it expands, there is an overcoming of factors of opposition and conflict; there is a transformation of them into differentiated aspects of a higher powered and more significant life.
  • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

.Taxonomy itself is never regulated, but is always the result of research in the scientific community.^ Ideally, such an endeavor would produce a nomenclature of agents that could be used relatively unambiguously by researchers in the field, resulting in clearer communications.

.How researchers arrive at their taxa varies; depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features to elaborate computer analyses of large amounts of DNA sequence data.^ The classification accuracy of methods using composition-based features might be influenced by a heterogeneous nucleotide composition present in the DNA sequence of the analyzed genomic fragment.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ Our standalone tool TACOA can also be easily installed and run on a desktop computer, therefore allowing researchers to locally analyze their metagenomic sequence data or integrate it into their pipelines.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ It is based on DNA data: you PCR-amplify the ITS region of the genome, cut it with restriction enzymes, then input your results for comparison to a database of known strains.

Phylogenetics

.Today, the alternative to the traditional rank-based biological classification is phylogenetic systematics, which is postulating phylogenetic trees (trees of descent), rather than focusing on what taxa to delimit.^ DNA chunks, the phylogenetic signal from the donor can still be detected if the HGT event is recent, rather than ancient [ 34 ].
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ It is increasingly common today to see classification schemes which are based not on historical ties but on current organizational affiliation or doctrinal similarity.
  • Levels of Classification of Faith Groups 25 September 2009 9:32 UTC www.adherents.com [Source type: FILTERED WITH BAYES]

^ The values are for the ROUNDED conservation status that are based on an algorithm to evaluate subnational conservation status ranks that systematically produces easier to interpret values without qualifiers or ranges (e.g.
  • NatureServe Canada Species at Risk Occurrence Data for the CanadianGeoSpatial Data Infrastructure (CGDI) 25 September 2009 9:32 UTC transfer.natureserve.org [Source type: Reference]

The best-known form of this is cladistics.
The results of cladistic analyses are often represented as cladograms. .It is held by cladists that taxa (if recognized) must always correspond to clades, united by apomorphies (derived traits) which are discovered by a cladistic analysis.^ A biological taxonomy is cladistic if all the taxa are clades.
  • Dictionary 21 January 2010 3:27 UTC www.dinosauria.com [Source type: FILTERED WITH BAYES]

.Some cladists hold that clades are poorly expressed in rank-based hierarchies and support the PhyloCode, a proposed ruleswork for the formal naming of clades, based on the model of the ICZN, ICBN etc.^ Some argue there should be a single system of rules for naming all organisms; a draft version of this proposed "Biocode" is provided at this web site.

^ Clades replace the old system of Linnean rankings such as Class, Order, etc.
  • Dictionary 21 January 2010 3:27 UTC www.dinosauria.com [Source type: FILTERED WITH BAYES]

^ Phylocode          A radical proposal to change the way we name organisms.

in rank-based nomenclature.

Numerical taxonomy

In numerical taxonomy, numerical phenetics or taximetrics, the taxonomy is exclusively based on cluster analysis and neighbor joining to best-fit numerical equations that characterize measurable traits of a number of organisms. .It results in a measure of evolutionary "distance" between species.^ Disruptive selection results in evolutionary changes and new species; once this occurs, however, the subpopulations enter into stabilizing selection evolution v.
  • Dictionary 21 January 2010 3:27 UTC www.dinosauria.com [Source type: FILTERED WITH BAYES]

This method has been largely superseded by cladistic analyses today; it is liable to being misled by plesiomorphic traits.

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.^ A decoratively woven fabric of a plaid pattern (sometimes called a sett) which is associated with a community in Scotland — a clan or family, a district, military, commercial, or other organization.
  • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

^ The similar body forms of Old World Monkeys and New World Monkeys are due to their having a common ancestor; their similar body forms are due to parallel evolution rather than convergence parsimony, principle of n.
  • Dictionary 21 January 2010 3:27 UTC www.dinosauria.com [Source type: FILTERED WITH BAYES]

^ Following a brief introduction on taxonomy and metadata (what I call content classification requirements), this article will focus on finding and utilizing such relationships in hierarchies.
  • Developing and Creatively Leveraging Hierarchical Metadata and Taxonomy - Boxes and Arrows: The design behind the design 21 January 2010 3:27 UTC www.boxesandarrows.com [Source type: General]

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.^ It should create the terms that don't exist (though, in general this shouldn't be required), then create or increment the term-taxonomy relationship (inefficient at the moment as it is db queries in a loop), then finally create the object-term-taxonomy relationships.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

."Fauxonomy" (from French faux, "false") is a pejorative neologism used to criticize folk taxonomies for their lack of agreement with scientific findings.^ THEN: One of the greatest obstacles to scientific agreement was lack of communication among scientists in all parts of the world..

^ Use the taxonomy browser, or perform a BLAST search to find sequences of interest.

.Baraminology is a taxonomy used in creation science which in classifying form taxa resembles folk taxonomies.^ Create a generic taxonomy and term API and schema that can be used for tags, post categories, link categories, and arbitrary future taxonomies.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ KEY THOUGHT: Policy taxonomies should ideally be organized into a "process arc" that clearly tells the story of the organization's creation and use of information.
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

.The phrase "enterprise taxonomy" is used in business to describe a very limited form of taxonomy used only within one organization.^ Only useful for taxonomies which are hierarchical.
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ The "Verb Taxonomy" that I'm pushing is a taxonomy (structured set of policies organized by relationships and principles) of policies that can use the noun taxonomies as input and automatically provide workflows and approvals.  It is important to provide a taxonomy of business policies that can be used to influence and govern the use of information across the enterprise.  This goes for SharePoint and any other tool in your organization.
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

^ Measurement is very difficult: As one panelist said, satellites paint pretty pictures that are often wrong, while point measurements are usually right, but not very useful.
  • From Nemo to Nano - TCS Daily 21 January 2010 3:27 UTC www.tcsdaily.com [Source type: FILTERED WITH BAYES]

.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.^ Another strategy would be to classify by type of control mechanism, algorithmic, rule-based, planner, fuzzy, neural net, machine learning, etc.

^ I would only use it when I can't think of a better pattern OR it is used with another pattern like Protected Variation or Indirection .
  • CSCI375: Questions and Answers on OO Design 25 September 2009 9:32 UTC cse.csusb.edu [Source type: FILTERED WITH BAYES]

^ Two types of methods are used for the taxonomic classification of environmental fragments: Composition-based and similarity-based-methods.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

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.[8] Clausewitz' 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.[9] .The use of taxonomies in the military extends beyond its value as an indexing tool or record-keeping template[10] -- for example, the taxonomy-model analysis suggests a useful depiction of the spectrum of the use of military force in a political context.^ Evaluating taxonomy tools provided by various vendors in the world right now.  What do these tools actually do?  Are they useful?  What is the scope of their taxonomy service and application?
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

[11]
.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.^ It will get all terms used in a given taxonomy or taxonomies.
  • #4189 (Taxonomy Schema and API) – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: General]

^ The way this works is that if the taxonomy that the term belongs to is .
  • /trunk/wp-includes/taxonomy.php – WordPress Trac 21 January 2010 3:27 UTC trac.wordpress.org [Source type: FILTERED WITH BAYES]

^ The taxonomy is intended to provide a structure for describing and categorizing the recovery mechanisms of complete systems as well as various design options.
  • A Taxonomy for Key Recovery Encryption 21 January 2010 3:27 UTC www.cs.georgetown.edu [Source type: Academic]

.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).^ Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown".
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ At each taxonomic rank, the classification accuracy (specificity and sensitivity) achieved for two different intrinsic classifiers: TACOA and PhyloPythia is given.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ Different individuals in the colony often take on specialised functions such as feeding, defence and reproduction - up to a thousand zooids may be found in a single colony.
  • http://www.marine-medic.com.au/pages/glossary.asp 21 January 2010 3:27 UTC www.marine-medic.com.au [Source type: FILTERED WITH BAYES]

[12]

Economic taxonomies

.Taxonomies are also often used to classify economic activity, including products, companies and industries.^ Any reference in the material to other organizations or companies, including their Internet sites, is not an endorsement or warranty of the services, information or products provided by those organizations or companies.

^ The terms classification, systematics, and taxonomy are often used interchangeably because they apply to the same concept of arranging things in their "correct" relationship.

^ Taxonomy Resources This site provides the list of all the taxonomic resources, including books, articles, and Web sites, used by GenBank's taxonomy group.
  • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

.Widely used industrial taxonomies include the International Standard Industrial Classification (ISIC); national and regional taxonomies such as the United States Standard Industrial Classification (SIC), the North American Industry Classification System (NAICS), Statistical classification of economic activities in the European Community (NACE), the United Kingdom Standard Industrial Classification of Economic Activities, the Russian Economic Activities Classification System (OKVED); and proprietary taxonomies such as the Industry Classification Benchmark and Global Industry Classification Standard.^ An excellent taxonomy resource that can be used to study classification.
  • Biology Resources - Shaleo Enterprises 25 September 2009 9:32 UTC users.rcn.com [Source type: Academic]

^ Unfortunately, several of the major sequence databases do not use a rigorous system for specifying taxonomy.
  • Matrix Science - Help - Mascot Search Fields 21 January 2010 3:27 UTC www.matrixscience.com [Source type: Reference]

^ English common names used in the list are by no means standardized but follow mostly those used by the IWC (International Whaling Commission).
  • ACS - American Cetacean Society 21 January 2010 3:27 UTC www.acsonline.org [Source type: FILTERED WITH BAYES]

.The international and national taxonomies are used by official statistical agencies.^ We have recently been awarded a research project by the French National Research Agency (ANR) entitled MEPHYSTAR for “Mechanics and statistical physics of rupture in heterogeneous materials” .

.The proprietary taxonomies are often used in the financial services industry to group similar investment vehicles and to construct sectorial stock market indices.^ The terms classification, systematics, and taxonomy are often used interchangeably because they apply to the same concept of arranging things in their "correct" relationship.

^ Evaluating taxonomy tools provided by various vendors in the world right now.  What do these tools actually do?  Are they useful?  What is the scope of their taxonomy service and application?
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

^ "Church", "sect", and "cult" are words often used to classify religious groups.
  • Levels of Classification of Faith Groups 25 September 2009 9:32 UTC www.adherents.com [Source type: FILTERED WITH BAYES]

Pavitt's Taxonomy classifies firms by their principal sources of innovation.

Safety taxonomies

The creation of taxonomies is very important in safety science. .For example there exist numerous taxonomies to classify and analyze human error and accident causes.^ There have been some examples of human remains placed on display.
  • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

.Examples of these include the Human Factors Analysis and Classification System based on Reason's Swiss Cheese Model, the CREAM (Cognitive Reliability Error Analysis Method), the taxonomy used by CIRAS (Confidential Incident Railway Analysis System) in the UK rail industry, and others.^ Compared to other less intuitive and more complex approaches, k -NN based methods have proven to yield competitive results in a large number of classification problems [ 25 - 28 ].
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ We estimated the classification accuracy of the presented method (TACOA) based on the leave-one-out cross-validation strategy.
  • BioMed Central | Full text | TACOA -Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach 25 September 2009 9:32 UTC www.biomedcentral.com [Source type: Academic]

^ Policy-based -- some sections of the taxonomy have special policies that invoked by the type of book identified.  Examples include the reference section (you can't check out the books), the current periodicals (ditto), and any attached historical archives (only open to scholars).
  • Mark Schneider's SharePoint Taxonomy and Governance Blog: Taxonomy 21 January 2010 3:27 UTC www.sharepointplan.com [Source type: FILTERED WITH BAYES]

[13]

Notes

  1. ^ Zirn, Cäcilia, Vivi Nastase and Michael Strube. 2008. "Distinguishing Between Instances and Classes in the Wikipedia Taxonomy" (video lecture). 5th Annual European Semantic Web Conference (ESWC 2008).
  2. ^ S. Ponzetto and M. Strube. 2007. "Deriving a large scale taxonomy from Wikipedia". Proc. of the 22nd Conference on the Advancement of Artificial Intelligence, Vancouver, B.C., Canada, pp. 1440-1445.
  3. ^ S. Ponzetto, R. Navigli. 2009. "Large-Scale Taxonomy Mapping for Restructuring and Integrating Wikipedia". Proc. of the 21st International Joint Conference on Artificial Intelligence (IJCAI 2009), Pasadena, California, pp. 2083-2088.
  4. ^ Jackson, Joab. "Taxonomy’s not just design, it’s an art," Government Computer News (Washington, D.C.). September 2, 2004.
  5. ^ Suryanto, Hendra and Paul Compton. "Learning classification taxonomies from a classification knowledge based system." University of Karlsruhe; "Defining 'Taxonomy'," Straights Knowledge website.
  6. ^ 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.
  7. ^ Grossi, Davide, Frank Dignum and John-Jules Charles Meyer. (2005). "Contextual Taxonomies" in Computational Logic in Multi-Agent Systems, pp. 33-51.
  8. ^ Calusewitz, Carl. (1982). On War, p. 141; "Defining 'Taxonomy'," Straights Knowledge website.
  9. ^ Cycorp: Structured information
  10. ^ 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.
  11. ^ 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.
  12. ^ Downie, Richard D. "Defining integrated operations," Joint Force Quarterly (Washington, D.C.). July, 2005.
  13. ^ Wallace,B, and Alastair Ross. Beyond Human Error: Taxonomies and Safety Science; (CRC Press 2006).

See also

References

.
  • Atran, S. (1993) Cognitive Foundations of Natural History: Towards an Anthropology of Science. Cambridge: Cambridge University Press.^ Burke Museum of Natural History, University of Washington, has a collection of tankas , many from the 20th century.
    • ArtLex's T-Te page 21 January 2010 3:27 UTC www.artlex.com [Source type: FILTERED WITH BAYES]

    ^ Edited by Daniel J. Howard and Stewart H. Berlocher [Cambridge: Oxford University Press, 1998].
    • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

    ^ The Cambridge Illustrated Dictionary of Natural History.
    • Primate Factsheets: Glossary 21 January 2010 3:27 UTC pin.primate.wisc.edu [Source type: FILTERED WITH BAYES]

    10-ISBN 0521438713 13-ISBN 9780521438711
  • Carbonell, J. G. and J. Siekmann, eds. (2005). Computational Logic in Multi-Agent Systems, Vol. 3487. Berlin: Springer-Verlag. 13-ISBN 978-3-540-28060-6
  • Clausewitz, Carl. (1982). On War (editor, Anatol Rapoport). New York: Penguin Classics. 10-ISBN 0-140-44427-0; 13-ISBN 978-0-140-44427-8
  • 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.^ By G. Ledyard Stebbins [New York: Columbia University Press, 1950].
    • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

    ^ By Todd F. Stuessy [New York: Columbia University Press, 1990].
    • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

    ^ Edited by R.G. Harrison [New York: Oxford University Press, 1993].
    • Evolution Library: Topic Page 25 September 2009 9:32 UTC www.pbs.org [Source type: Academic]

    10-ISBN 0-887-06653-4; 13-ISBN 978-0-887-06653-5; OCLC 15856738
  • *Marcello Sorce Keller, "The Problem of Classification in Folksong Research: a Short History", Folklore, XCV(1984), no. 1, 100-104.
  • Chester D Rowe and Stephen M Davis, 'The Excellence Engine Tool Kit'; ISBN: 978-0-615-24850-9

External links


Simple English

Taxonomy is a science. It is about the classification of all things living. Although it is most commonly used in biology, it can be used in other types of classification too. Taxonomy is used with different ranks, the lowest is a species. There can also be sub-species. An organism is a species if two organisms of the same kind can mate. This name is the scientific classification of that species. The name is the same all over the world, so that when scientists from different places talk or write about the living thing, they can understand each other.

The highest rank in the domain of living things is the Kingdom. Each kingdom has many smaller groups in it, called Phyla: see List of animal phyla. Each Phylum has more smaller groups in it, called Classes. This pattern looks like branches on a tree with smaller branches growing from them. Each species is put into a group because of what it does, how and what it eats, special body parts, and so on. At the end of the pattern, the groups (Genera) are very small. Then each species in the Genus is given its own name. When someone writes about a living thing and uses this name, they only write the Genus name and the species name, like this:

Felis silvestris catus (domestic cat)

When someone writes about this animal, the first time they write its name they will write Felis silvestris catus. After the first time they write its name, they will only write the first letter of the Genus, so they will write F. silvestris catus. This is known as binomial nomenclature, because it is a way to describe organisms using two names, the first is the Genus name, and the second is the adjective that denotes the specific species of that genus.

These are the major groups (ranks) used in taxonomy:

Kingdom --> Phylum --> Class --> Order --> Family --> Genus --> Species

A mnemonic, or a saying to help a person remember something, for that is "King Phillip Came Over From Greater Spain","King Phillip Came Over For Good Spaghetti", and King Phillip Cried Out "For Goodness Sake".

Other pages


Citable sentences

Up to date as of December 24, 2010

Here are sentences from other pages on Taxonomy, which are similar to those in the above article.








Got something to say? Make a comment.
Your name
Your email address
Message