Creating Taxon Lists

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

Step 1: create and save your taxon list file

Make sure that you have an internet connection before starting Phenote+ as the software will need to download updated ontology files when available.

1. Start up Phenote+, and check that you are using the Taxon configuration of Phenote (to check, go to Settings>Set Configuration, and confirm that ‘phenoscape_taxon’ is chosen).
2. Create and save your file using File>Save, naming the file for the publication and including "taxon-list" in the name (e.g. Smith-2008-taxon-list).

Step 2: make a list of examined taxon names

1. Choose the Annotation Table panel and click the ‘+’ button to add an entry to the taxon list: the first row will be gray. Select the row by clicking on it; it will turn blue.
2. Go to: Annotation Editor panel, go to Publication, and type in the author(s) and year for the publication (e.g., Smith 2008), and hit enter/return. Note: this step can be done in bulk when the the taxon list is completed.
3. Go to Publication Taxon, and paste the taxon name into this field that you copied from the pdf Material and Methods list and hit enter/return.
4. Now, paste the same taxon name into the “Valid Taxon” field. Because the "Valid Taxon" field is linked to the taxonomy ontology, you should see a drop-down menu appear with the taxon name; hit enter/return, and note that the name appears in the spreadsheet. (If the name does not appear in the drop-down box, see Issues and special cases, below).
5. Repeat steps 1-3 for the entire taxon list.

Note: Be sure to hit enter/return after typing or pasting data, otherwise Phenote+ may not record the entry.

Issues and special cases

1. Synonyms: for example, the paper that you are annotating has “Danio devario” in the Materials list. Paste this species name in the Valid Taxon field, and you will notice that “Danio devario[syn]” appears in the drop down menu. When you chose this, notice that the valid name “Devario devario” is automatically entered. You should record "Danio devario" in the Publication Taxon list as a record of the name used by the author in that publication.
2. If the taxon name isn’t in the drop down menu, type the name into the field “Publication Taxon”. You may add any notes (e.g. “Name appears to be misspelled”) in the taxon comments.
3. If a taxon is not identified to species in the materials list, then leave the Valid Taxon field blank. For example, Arius sp. might be listed in the materials list; do not choose Arius from Valid Taxon; simply type Arius sp. in Publication Taxon. Likewise, an author may indicate uncertainty in a species identification (e.g., Devario cf. devario or Devario aff. devario) and therefore Valid Taxon should be left blank.**NB: Do not choose a taxon name from the drop down menu if it includes citation to another publication; using the example above, you might find Arius sp. (Jones 1990) in the drop down menu, but don't choose this as the Valid Taxon because it refers to an Arius sp. in another publication. By leaving the Valid Taxon field blank, Peter or Wasila will know to add Arius sp. (Smith 2008) to the taxonomy ontology, and we will update this file at a later time with this Valid Taxon name.
4. If a specimen is listed as a holotype or paratype, record this in the Taxon Comments field.

Hints

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

Step 3: add voucher specimens to the taxon names

1. When you are finished adding all of the taxa, go to the 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).
2. To add a specimen, click the ‘+’ button in the Specimens panel. 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.
3. 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).
4. If 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 used in the paper. Make a note in Taxon Comments whenever a paper lists a code not present in Phenote+. We will add the new code to Phenote+ later.
• Likewise, if you can't find a museum name listed in the drop-down menu, make a note 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.
• Occasionally, a specimen entry will be missing a collection code (e.g., no museum is listed next to the species name; or the specimen is an uncataloged aquarium specimen). Just enter the taxon name, leave Specimens fields blank, and make a comment in the Taxon Comments field.
• If a paper has multiple consecutive lots containing specimens of the same species, the individual lots should be entered separately only when there are less than 10 lots listed; for example:

1. Materials List has KIZ 846140-846142; Enter into Phenote as: KIZ 846140, KIZ 846141, KIZ 846142
2. Materials List has AMNH 20050 – 20075; Enter into Phenote as: AMNH 20050 – 20075

When you finish a taxon list:

1. Copy the file to "Taxon lists (phenote+)" folder on phenoscape-data
2. Update the publications list on Google docs: indicate completion in the Taxon List column. See below for example:
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3. Send email to taxon expert (ask Paula or Wasila if you don’t know), and always cc: the phenoscape-curators mailing list (Phenoscape-curators@lists.sourceforge.net). Attach the Phenote+ taxon list. Here is a sample email:

"Dear Curator,

Attached is a copy of the taxon list for Schaefer 1990 that I just completed. You will notice that the list of publication taxa is complete (copied and pasted from paper), but there are a number of valid taxa that are not apparently in the ontology (i.e. a valid name does not pop up when publication taxon name is entered in valid taxon field).

I am sending this to you (taxon expert for catfish) to choose the appropriate valid taxon name and to update this file. Please notify Peter Midford if any new names are required in the Taxonomy Ontology.

After you are done, please post the updated Taxon list for this paper to the “Taxon lists (phenote+)" folder on phenoscape-data.

Thank you!

Your name (Paula’s lab)"