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You can add a set of taxonomic names to your project in one go by clicking on the "Upload taxon batch" link and using the displayed form to upload a properly formatted taxon file.

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Figure 2.7. The Taxa tab showing all ways to edit taxa.

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.


To batch update the extinct status of taxa in your project, click on the Taxa tab and then on the "Edit extinct taxa" button (Fig. 2.5). You can drag and drop taxa from one list to the other and move taxa in batches from one side to the other.

Figure 2.78. Editing taxon extinct status in batch


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 then make adjustments by hand for taxa that do not fit that rank.

Figure 2.89. The taxon editing page showing the form fields for ranks.  Here only the genus and species are completed.


To view the specimen directory click on the Specimens tab in the project tool tab bar.

Figure 2.910. Portion of the specimen directory.  Note examples of unvouchered (top arrow) and vouchered (bottom arrow) specimens, the latter have a collection and catalog number.


To edit a specimen, find it using any of the provided tools - search or browse by first letter of name - and click on the specimen's "edit" button. You can then change any of the values of the specimen using the provided form. Note that changes made to a specimen will affect all media that refer to it.

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Figure 2.1011. Specimen entry form for vouchered specimens


Click on the 'Add specimen batch' button in Fig. 2.910. You will be taken to a page where you can upload a tab- or comma-separated file with your specimen information from your computer. Instructions on the fields and their contents are on this page as well.

Figure 2.1112. Batch upload page for specimens


Unlike most other MorphoBank data, project bibliographies can be shared across multiple projects. Thus you can establish a single bibliography and cite it across all of your MorphoBank-hosted workspaces. The process of linking projects together so they can share a bibliography is described below.

Figure 2.1113. Project bibliography list


The bibliography can be navigated alphabetically by author's name or searched. If you edit an existing reference that is already used in citations for your project data, then any changes made will automatically propagate to the citations. As shown below, if you try to delete a reference that is used by existing citations you will be shown the list of items (taxa, characters, media, etc.) that cite the reference and given the option to shift the citations to another reference.

Figure 2.1214. Warning when attempting to delete a bibliographic reference that is in use to document for matrix cells or media.


You can add a reference to your bibliography by clicking on the "Add new bibliographic reference" button in the upper-right-hand corner of the bibliography display. You will see a form like the one below. Follow the data-entry guidelines shown on the form and in the tips visible when mousing over the "(help)" buttons above each form field, filling in as much information as you can. Then click the "save" button.

Figure 2.1315. Editing a single bibliographic reference


After you have exported your file in EndNote XML format from your reference manager, open your MorphoBank bibliography, click on the "Import Endnote XML file" button in the upper-right-hand corner of the bibliography display, then choose the XML file on your computer using the file-browse button.

Figure 2.1416. Importing references in batch