Creating Taxon Lists

The following instructions provide details on how to build a taxon list from a published materials list using Phenote+.

Create and save your taxon list file

Create a new folder and name it for the publication you are annotating (e.g., Smith-2008, Smith&Gomez-2008, Smith-etal-2008). You can either do this from the Finder/Windows Explorer or (later) from the file dialog box if you know how.

Start Phenote. Make sure that you are using the Taxon configuration of Phenote (to check, go to Settings>Set Configuration, and confirm that ‘phenoscape_taxon’ is chosen).

Create your file using File>Save, naming the file for the publication with the extension ‘.tab’ (e.g. Smith-2008.tab).

Make a list of examined taxon names

Choose the Taxon List tab and click the ‘+’ button to add an entry to the taxon list: the first line will be gray.

Go to: Annotation Editor, go to “Valid Taxon” and add a taxon name. The paper that you are annotating has “Danio devario” in the Materials and Methods. Begin typing this species name, and you will notice that “Danio devario[syn]” comes up in drop down menu. When you chose this, notice that the valid name “Devario devario” is automatically entered. If the taxon name isn’t in the drop down, type the name into the field “Publication Taxon”. You may add any notes (e.g. “Name appears to be misspelled”) in the taxon comments.

Hints

• If the genus is misspelled in the paper, sometimes typing just the species name will find the correct binomial.
• In the Taxon List tab, the ‘-‘ button will delete the current entry.
• All data entry can be done in the Annotation Table by double or triple clicking cells until a blinking cursor appears.

Note: Type the taxon name in the "Publication Taxon" field when you encounter the following situations:

• Binomial (Genus species) does not appear in Valid Taxon drop-down menu
• "Genus sp." type name is given (e.g., Danio sp.; Devario sp. Big Spot)
• Uncertainty in species identification is indicated (e.g., Danio cf. devario; Danio aff. devario)

Add voucher specimens to the taxon names

When you are finished adding all of the taxa, go to Specimens tab (if not there, choose View:Show:Annotation:Specimens from the main menu and the tab will be added, but it may be floating around behind your main screen).

To add a specimen, click the ‘+’ button in the Specimens tab. Now click three times in the first cell in the collection code column (you will see a blinking cursor) and start typing the collection code (for example, MNHN). When the desired collection abbreviation appears in the menu, select it from the menu or type the abbreviation and hit return/enter. Now double-click on the adjacent cell in the Specimen ID column, and a box for entering text will appear – enter the ID (lot number) and press enter/return. You may want to copy and paste this from the pdf of the paper that you are annotating in order to avoid making mistakes (but double-check that you are not pasting extra characters). When there are multiple specimens listed for a taxon, use the ‘+’ button to add another row, and select cells in the second row to enter the collection code and specimen id.

Notes:

• If you don't find the appropriate museum abbreviation, you can begin typing the full name of the museum (e.g., Los Angeles County Museum of Natural History) to see if the museum is listed under a different code than the one reported in the paper. If you still don't find the museum in the drop-down menu, make a note in the Taxon Comments field that the museum name is missing.
• Occasionally, a specimen entry will be missing a collection code (e.g., no museum is listed next to the species name). Just enter the taxon name, and make a comment in the Taxon Comments field.
• Specimens will sometimes be listed as 'uncataloged' (e.g., MNHN uncat.); in this case, choose the appropriate museum abbreviation and type 'uncat.' in the Specimen ID field.