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.
Hints
- 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”).
Notes:
- 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:

- 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:
“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)”