XBio:D Taxonomic Data Model - Revision history

Jcora: /* xBio:D Basic Tenets for Taxonomy */

2015-03-11T14:05:29Z

‎xBio:D Basic Tenets for Taxonomy

Jcora: /* xBio:D Basic Tenets for Taxonomy */

2015-02-24T15:35:19Z

‎xBio:D Basic Tenets for Taxonomy

Jcora at 23:04, 23 February 2015

2015-02-23T23:04:54Z

Jcora at 22:41, 23 February 2015

2015-02-23T22:41:32Z

Jcora at 22:40, 23 February 2015

2015-02-23T22:40:55Z

Jcora at 22:39, 23 February 2015

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Jcora at 22:36, 23 February 2015

2015-02-23T22:36:24Z

Jcora at 22:34, 23 February 2015

2015-02-23T22:34:22Z

Jcora: Created page with "'''Introduction''' This page will provide information on the xBio:D taxonomic data model. Only users with taxonomic permissions and possess the taxonomic authority upon a cer..."

2015-02-23T22:31:02Z

Created page with "'''Introduction''' This page will provide information on the xBio:D taxonomic data model. Only users with taxonomic permissions and possess the taxonomic authority upon a cer..."

New page

'''Introduction'''

This page will provide information on the xBio:D taxonomic data model. Only users with taxonomic permissions and possess the taxonomic authority upon a certain group are able to manage taxonomies, so if you would like to contribute to the xBio:D taxonomic resources, please contact [mailto:hol-help@osu.edu hol-help@osu.edu] and request permission.

== xBio:D Taxonomic Data Model Basics ==
The xBio:D taxonomic data model is modeled using a [http://en.wikipedia.org/wiki/Tree_%28graph_theory%29 tree graph] in which nodes correspond to taxonomic concepts and the edges are taxonomic relationships. Taxonomic names are treated as entities within a node that corresponds to identities for a taxon with at most one being valid.
[[File:Taxonomic_concepts_example.png|none|frame|Example of taxonomic data model]]

An analogy that may be helpful to understand the data model is to imagine a species as a model of car. A model can have multiple spelling, different designations, and misspellings from shoddy catalogs, e.g., Corolla 2-door, Corrolla 4-door, Toyota Corolla DX, etc., but they are all the same model and thus the same concept. Each of the model spellings can be viewed as taxonomic names and the model itself is the concept. Let's say that the one model spelling that is preferred is "Toyota Corolla" and we consider this as the valid name for the model. There is another model, the "Toyota Sprinter", that is essentially the same car model as the "Toyota Corolla", but since it has a fundamentally different name, we treat it as a separate model. However, we deem both models to represent the same model, and since the "Toyota Corolla" name is older, we consider that to be the valid model. To map this example to the above graph, ''[http://hol.osu.edu/index.html?id=2995 Telenomus ovivorus]'' is equivalent to "Toyota Corolla" and ''[http://hol.osu.edu/index.html?id=3146 Telenomus turkarkandas]'' is equivalent to "Toyota Sprinter". "Toyota Corolla" is synonymous with "Toyota Sprinter", but since the "Corolla" name is older, it is the senior synonym while the "Sprinter" is a junior synonym. "Toyota" is the brand for the model, and can be viewed as being equivalent to ''[http://hol.osu.edu/index.html?id=605 Telenomus]'', the genus in the above graph. "Toyota", the brand, has many other car models that are made by, or members of, it with the "Toyota Corolla" being one. The brand "Toyota" is a member of the manufacturer "Toyota" in a similar way that the genus ''Telenomus'' is a member of the subfamily [http://hol.osu.edu/index.html?id=592 Telenominae] and so one until eventually you reach the kingdom, Animalia.

To maintain this analogy, let's say that the "Toyota Corolla" model is sold off to "Chevrolet". Then, a new name is added to the model concept, "Chevrolet Corolla", which becomes the valid name while the other names for the model become obsolete. "Toyota Sprinter" is still synonymous for the "Chevrolet Corolla" but is not given the name "Chevrolet Sprinter" because the name is never to be used. Since "Toyota" is no longer the brand of the "Corolla", the new parent for the model is "Chevrolet". This type of action is equivalent to a species being transferred from one genus to another.

[[Category:Database Manager]]
[[Category:FAQ]]

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 * Species concepts should always include the original spelling. This is the best way to identify the correct species when secondary homonymy or obscure subsequent combinations are used. Properly formatted author names should always be used with an ampersand (&) delimiting the last from the next to last author (see ''[http://hol.osu.edu/index.html?id=156200 Maaminga]'' Early, Masner, Naumann & Austin in HOL).
 * Only the original combination of a species should be marked as a "junior homonym", even if the subsequent combination not the original name is the homonymous one.
-* Classifications should be based on the most recent published literature for a group. This avoids the pitfalls of when an expert knows best but doesn't publish resulting in a perpetual limbo. Publishing always solves any confusion created by "novices".
+* Classifications should be based on the most recent published literature for a group. This avoids pitfalls associated with an expert who doesn't publish their results creating a perpetual state of limbo within a group. Publishing always solves any confusion created by "novices".
 * The use of subgenera or subgeneric combinations as valid is discouraged but allowable. Retrieving a list of species within a subgenus that is treated as a synonym of a genus can still be achieved by making the parent taxon of the species an invalid subgenus (see ''[http://hol.osu.edu/index.html?id=316488 Cicindela (Calochroa)]'' in HOL).
 * The DB Manager will give you warnings when certain taxonomic names are unusual for a given rank, parent concept, etc. Please take heed of these warnings and only override them when you are confident that the warning does not apply in the current instance.

@@ Line 22: / Line 22: @@
 * Classifications should be based on the most recent published literature for a group. This avoids the pitfalls of when an expert knows best but doesn't publish resulting in a perpetual limbo. Publishing always solves any confusion created by "novices".
 * The use of subgenera or subgeneric combinations as valid is discouraged but allowable. Retrieving a list of species within a subgenus that is treated as a synonym of a genus can still be achieved by making the parent taxon of the species an invalid subgenus (see ''[http://hol.osu.edu/index.html?id=316488 Cicindela (Calochroa)]'' in HOL).
 [[Category:Database Manager]]
 [[Category:FAQ]]

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 The xBio:D taxonomic data model is modeled using a [http://en.wikipedia.org/wiki/Tree_%28graph_theory%29 tree graph] in which nodes correspond to taxonomic concepts and the edges are taxonomic relationships. Taxonomic names are treated as entities within a node that corresponds to identities for a taxon with at most one being valid. This data model can accommodate all codes of nomenclature, like the [http://www.nhm.ac.uk/hosted-sites/iczn/code/ ICZN], while being amenable to the taxonomic and nomenclatural acts that are common to systematics.
 [[File:Taxonomic_concepts_example.png|none|frame|Example of taxonomic data model]]
 An analogy that may be helpful to understand the data model is to imagine a species as a model of car. A model can have multiple spelling, different designations, and misspellings from shoddy catalogs, e.g., Corolla 2-door, Corrolla 4-door, Toyota Corolla DX, etc., but they are all the same model and thus the same concept. Each of the model spellings can be viewed as taxonomic names and the model itself is the concept. A nickname for the car model like "the goat" can be viewed like a common or vernacular name. People may use the name amongst each other, but it will never be the formal name of the model.

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 [[File:Taxonomic_concepts_example.png|none|frame|Example of taxonomic data model]]
-An analogy that may be helpful to understand the data model is to imagine a species as a model of car. A model can have multiple spelling, different designations, and misspellings from shoddy catalogs, e.g., Corolla 2-door, Corrolla 4-door, Toyota Corolla DX, etc., but they are all the same model and thus the same concept. Each of the model spellings can be viewed as taxonomic names and the model itself is the concept. A nickname for the model like "the goat" can be viewed like a common or vernacular name. People may use the name amongst each other, but it will never be the formal name of the model.
+An analogy that may be helpful to understand the data model is to imagine a species as a model of car. A model can have multiple spelling, different designations, and misspellings from shoddy catalogs, e.g., Corolla 2-door, Corrolla 4-door, Toyota Corolla DX, etc., but they are all the same model and thus the same concept. Each of the model spellings can be viewed as taxonomic names and the model itself is the concept. A nickname for the car model like "the goat" can be viewed like a common or vernacular name. People may use the name amongst each other, but it will never be the formal name of the model.
 Let's say that the one model spelling that is preferred is "Toyota Corolla" and we consider this as the valid name for the model. There is another model, the "Toyota Sprinter", that is essentially the same car model as the "Toyota Corolla", but since it has a fundamentally different name, we treat it as a separate model. However, we deem both models to represent the same model, and since the "Toyota Corolla" name is older, we consider that to be the valid model. To map this example to the above graph, ''[http://hol.osu.edu/index.html?id=2995 Telenomus ovivorus]'' is equivalent to "Toyota Corolla" and ''[http://hol.osu.edu/index.html?id=3146 Telenomus turkarkandas]'' is equivalent to "Toyota Sprinter". "Toyota Corolla" is synonymous with "Toyota Sprinter", but since the "Corolla" name is older, it is the senior synonym while the "Sprinter" is a junior synonym. "Toyota" is the brand for the model, and can be viewed as being equivalent to ''[http://hol.osu.edu/index.html?id=605 Telenomus]'', the genus in the above graph. "Toyota", the brand, has many other car models that are made by, or members of, it with the "Toyota Corolla" being one. The brand "Toyota" is a member of the manufacturer "Toyota" in a similar way that the genus ''Telenomus'' is a member of the subfamily [http://hol.osu.edu/index.html?id=592 Telenominae] and so one until eventually you reach the kingdom, Animalia.