Taxonomy is a critical part of any MorphoBank project. You cannot create matrices from scratch or specimen records without loading taxonomic names. The sections below describe MorphoBank's tools for taxon loading and management.
MorphoBank maintains a central directory of taxonomic names for each project. The directory lists each taxon once - no duplicates are allowed. Matrices and specimens using the same taxon are actually referring to a single entry in the taxonomic directory. This means that if you modify a taxon, the change will be reflected everywhere it is used in your project.
To view the taxonomic directory click on the
Taxa link in the project sub-navigation
bar.
You can view lists of taxa by first letter of their name using the "Show taxa whose..." bar as shown in the above figure. Taxa may be edited or deleted using the respective buttons. Note that if you delete a taxon, it will be removed from all matrices and specimen records that refer to it.
![[Warning]](file:/Applications/oxygen/frameworks/docbook/xsl/images/warning.png) | Warning |
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| Think before you delete a taxon! Deleting a taxon will cause it to be removed from all matrices and specimen records that refer to it. It will also cause all matrix scores, cell images and cell media labels associated with the taxon to be deleted. |
You may view taxa by partition or matrix using the "Show by taxa partition or matrix" drop-down menu.
You can search taxa by entering any part of the taxon name into the search box and clicking on the "search" button. Partial matches can be made by using the asterisk ("*") wildcard character. For example, to find all taxa starting with the letters 'aeto' search on 'aeto*'
At least one element of the taxonomic name must be specified. While some users may prefer to express complete names, from kingdom to subspecies, this is not required. All fields are optional.
To add taxa one at a time, click on the "Add new taxon" link in the upper-right hand corner of the tab, then fill in all applicable fields in the new taxon form and click on the "save" button. If the taxon is extinct check the "is extinct" checkbox. Taxa so marked will appear in MorphoBank with an asterisk ("*") before the name.
You can add a set of taxonomic names to your project in one go by clicking on the "Upload taxa batch" link and using the displayed form to upload a properly formatted taxon file.
A taxon file is simply a specially formatted tab-delimited text file. Each line of a taxon file represents a single taxon and is split into several columns, one for each component of the taxon, separated by TAB characters. The first line of the file is reserved for column labels. You must label your columns using the following labels: Kingdom, Phylum Class, Subclass, Order, Suborder, Superfamily, Family, Subfamily, Genus, Species, Subspecies, Author, Year and Notes.
The labels must be entered exactly as displayed above or your file will be rejected. You may omit any column not used by your data - all columns are optional. However, at least one of the name columns must be defined. The "notes" column is intended for taxon-specific notes you wish to associate with the new taxon. You may enter the author with year separated by comma (eg. "Schwartzenegger, 1879"), or you may place the year in the separate "year" column. Surround the author's name with parentheses if you wish it to display that way.
Although any text editor may be used to create taxon files, it is usually more convenient to employ spreadsheet software such as OpenOffice or Microsoft Excel and a sample file to get you started. Note that you cannot upload Excel files to MorphoBank. You must save your Excel files as tab-delimited text before uploading them to MorphoBank.
When uploading a NEXUS file to create a matrix, all taxa present in the file are automatically added to the taxonomic directory. This is a collateral effect of importing a matrix but can be used to batch add taxonomy and is especially convenient if your data is already in NEXUS format.
The NEXUS format treats taxonomic names as simple strings of text. There is no formal delineation of the hierarchical elements present in a taxon. Because hierarchy information is not present in NEXUS files MorphoBank assumes that the first word in each taxa is the operational taxonomic unit, and that each subsequent word is one level below in the hierarchy. For example, if the OTU is set to genus, then all names will be interpreted as genus/species/subspecies. This is an admittedly imperfect system, it performs acceptably for many data sets. Unless your taxonomy is uniform you will need to do some clean up after importing a NEXUS file into MorphoBank.
To edit a taxon, find it using any of the provided tools - search, browse by first letter of name or list by matrix or partition - and click on the taxon's "edit" button. You can then change any of the values of the taxon using the provided form. Note that changes made to a taxon will affect all matrices and specimens that refer to it.
In MorphoBank, the OTU function allows you to set a rank for the taxa in your matrix. Each matrix in your project has a default OTU that applies to all taxa without an otherwise specified OTU. If you want to ensure that a taxon always has a specific OTU you must set it in the taxon form when adding or editing. If you have OTUs of different ranks and are starting a project by uploading a matrix, select the rank most commonly found and the then make adjustments by hand for taxa that do not fit that rank.