Difference between revisions of "App/otu"

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OTUs are the core objects in the database. They represent taxonomic concepts of any level or rank. Most other objects are attached or referenced through an OTU.
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Data in mx are primarily tied to OTUs, which in turn are linked into a taxonomic names hierarchy. The names are individually used in different contexts (e.g. in public a manuscript name won't be shown, in matrices the matrix name will be used if provided, etc.).  In mx these names are often displayed together and can be identified by their colour:
[[normal.jpg]]
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==New==
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There are two ways to create OTUs. Both start by clicking on the New OTU link.
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  black name (comes from the link to a taxon name)
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  <span style="color:blue;">blue name </span> (comes from the OTU 'name' field)
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  <span style="color:green;">green name </span> (comes from the OTU 'matrix name' field)
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  <span style="color:red;">red name </span> (comes from the OTU 'manuscript name' field)
  
# You may create a single OTU by filling out the form.
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This system allows you to create OTUs in the absence of a taxonomic name hierarchy if needed, and it allows any naming convention to be used (e.g. lab codes, etc.). Some general guidelines/considerations are useful in practice:
# You can create multiple OTUs at once by clicking on the Include all children? checkbox. This creates an OTU for the chosen taxon name, and every child. Be careful- you may be creating more than you wish, and at present you have to delete OTUs one at a time.
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# If you a) have a taxonomic name hierarchy and b) want to represent a 1:1 match of concept to name then simply select the appropriate taxonomic name and do not provide a OTU name
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# If you don't have a 1:1 match, or want to include multiple concepts for a given name identify your OTUs to the finest level within the taxonomic hierarchy by choosing a the closest taxon name, then repeat the working name as an OTU name. Your name might then look like this: '''''Aus'' <span style="color:blue;">Aus sp23</span>'''.
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# While it is not necessary to tie an OTU to the taxonomic hierarchy you can benefit from doing so as some data (e.g. content) are organized by this hierarchy
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# While anything is permitted names should ''not'' typically formed like '''''Aus'' <span style="color:blue;">bus</span>''' bur rather like this: '''''Aus'' <span style="color:blue;">Aus bus</span>''', i.e. include the redundancy in the OTU name. Remember you are not reading the name across from left to right, you're reading up to 4 different names concatenated for display purposes.  Components of that concatenation are shown individually in their respective places.
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# In collaborative labs it's useful to fill in the Sensu/concept field so as to keep OTUs distinguishable by something other than IDs
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# Consider making ample use of OTU groups as you create OTUs
  
== Edit ==
 
  
=== Published names vs. Containing taxon ===
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== OTU Application help ==
  
You can tie your OTU to a published taxonomic name by selecting a taxon name via the blue picker at the top when you edit that OTU. If your OTU represents that taxon name that’s all you need to do. If your OTU is a child of that taxon name you can click the “Is child of published name?” check box. Note that we recently merged the functionality of is/is child to a single dropdown.
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{{Special:Prefixindex/App/otu/}}
 
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=== Manuscript Names ===
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Do not place manuscript names in the name field. If you are describing a new species in an currently available genus you should enter the genus name and “new species” in name, field and the full species epithet in the manuscript name field. OTU names are/will be routinely displayed for public use in some cases, and thus it is very important to not include manuscript names in that field.
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=== List ===
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By default all the OTUs for the current project are listed. In most cases you will not want to see this list, but rather a grouped-list. You can create as many OTU groups as you want in the Groups + Templates tab. When there select a group as a default and when you return to the OTU tab you’ll only see those group members. At present the OTU default group is reset every time you enter a project.
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There are various possible names for OTUs. These are color-coded in the list as follows:
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<b>Taxon Name <span style="color: blue;">Otu Name</span> <span style="color: red;">Manuscript Name</span>  <span style="color: green;">Matrix Name </span> <span style="color: silver;">(Containing Taxon name)</span></b>
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Latest revision as of 16:46, 26 April 2011

Data in mx are primarily tied to OTUs, which in turn are linked into a taxonomic names hierarchy. The names are individually used in different contexts (e.g. in public a manuscript name won't be shown, in matrices the matrix name will be used if provided, etc.). In mx these names are often displayed together and can be identified by their colour:

 black name (comes from the link to a taxon name)
 blue name  (comes from the OTU 'name' field)
 green name  (comes from the OTU 'matrix name' field)
 red name  (comes from the OTU 'manuscript name' field)

This system allows you to create OTUs in the absence of a taxonomic name hierarchy if needed, and it allows any naming convention to be used (e.g. lab codes, etc.). Some general guidelines/considerations are useful in practice:

  1. If you a) have a taxonomic name hierarchy and b) want to represent a 1:1 match of concept to name then simply select the appropriate taxonomic name and do not provide a OTU name
  2. If you don't have a 1:1 match, or want to include multiple concepts for a given name identify your OTUs to the finest level within the taxonomic hierarchy by choosing a the closest taxon name, then repeat the working name as an OTU name. Your name might then look like this: Aus Aus sp23.
  3. While it is not necessary to tie an OTU to the taxonomic hierarchy you can benefit from doing so as some data (e.g. content) are organized by this hierarchy
  4. While anything is permitted names should not typically formed like Aus bus bur rather like this: Aus Aus bus, i.e. include the redundancy in the OTU name. Remember you are not reading the name across from left to right, you're reading up to 4 different names concatenated for display purposes. Components of that concatenation are shown individually in their respective places.
  5. In collaborative labs it's useful to fill in the Sensu/concept field so as to keep OTUs distinguishable by something other than IDs
  6. Consider making ample use of OTU groups as you create OTUs


[edit] OTU Application help

App/otu/editApp/otu/edit pageApp/otu/index
App/otu/newApp/otu/showApp/otu/show codings
App/otu/show compare contentApp/otu/show contentApp/otu/show material
App/otu/show matrix sync
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