Creating Taxon Lists
The following instructions provide details on how to build a Taxon List from a published materials list using Phenex.
Step 1: create the file for your taxon list
Make sure that you have an internet connection before starting Phenex, because the software needs to download updated ontology files.
- Create and save your file using File>Save, naming the file for the publication and appending .xml to the end (e.g. Smith_2008.xml).
Step 2: make a list of taxon names from the Materials section of the publication
- Choose the Taxa panel and click the ‘+’ button to add an entry to the taxon list: the first row will be gray. By clicking on the column within the row you will be able to add data.
- Go to: Data Set panel, go to Publication, and type in the author(s) and year for the publication (e.g., Smith 2008), and hit enter/return.
- Go to Taxa panel and click into the Publication Taxon field. Paste the taxon name into this field that you copied from the pdf Material and Methods list and hit enter/return.
- 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, then leave it blank).
- Repeat step 3 for the entire taxon list, adding a new row by clicking the "+" button for each new entry.
Note: Be sure to hit enter/return after typing or pasting data, otherwise Phenex may not record the entry.
Issues and special cases
- 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.
- If the taxon name isn’t in the drop down menu of Valid Taxon field, make sure the taxon name is in the field “Publication Taxon” and continue to adding the next taxon. You may add any notes (e.g. “Name appears to be misspelled”) in the Comments field.
- 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.
- 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
- When you are finished adding all of the taxa, go to the Specimens for Taxon tab.
- To add a specimen, click the ‘+’ button in the Specimens panel. Now click twice in the first cell in the Collection 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).
- 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.
Requests for missing museum abbreviations: Use the Fish Collection Codes spreadsheet on Google Docs to request the addition of missing codes, or request addition of synonyms of an existing code:
- Add code and full name of museum to the *last line* of the spreadsheet. If you are adding a synonym to an existing collection code, use columns C or D as necessary
- In the Status field, type "pending", and record the date of request and your initials in the Request Notes field.
- In the Phenex file, make a note in the Publication notes field (under "Data Set" tab) describing your request (e.g., "museum code XYZ missing; code added to Google Docs on 8/3/2008, Your Initials").
- Try typing the full name of the museum if you can't find the appropriate museum code ( (e.g., Los Angeles County Museum of Natural History instead of LACMNH). See instructions on requesting missing museum codes, if this is necessary.
- Look at the list of existing specimen codes in the Google doc - it may simply be misspelled.
- Search for the author's definition of that abbreviation in the publication, and then see if the full name of the collection is in our list but under another name.
- 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:
- Materials List has KIZ 846140-846142; Enter into Phenote as: KIZ 846140, KIZ 846141, KIZ 846142
- Materials List has AMNH 20050 – 20075; Enter into Phenote as: AMNH 20050 – 20075
When you finish a taxon list:
- Copy the file to the appropriate folder in the Phenoscape data repository.
- Update the curation log to indicate the work done on the taxon list. See below for example: Error creating thumbnail: Unable to save thumbnail to destination
- Send email to taxon expert (ask Paula or Wasila if you don’t know), and always cc: Paula and Wasila. Here is a sample email:
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.
Your name (Paula’s lab)"