Update Taxon Lists
The following are instructions on how to update a taxon list for taxonomy and submit requests for needed taxonomic names in the TTO.
Obtain the xml file from the Phenoscape data repository
Open file in Phenex
Make sure that you have an internet connection before starting Phenex as the software will need to download updated ontology files if available.
Start up Phenex and open the xml file using File>Open.
Choose the Taxon perspective by going to Window>Taxon. This will display only the Taxon panels (Taxa, Specimens, Term Info) in Phenex.
Review Taxon List
Taxon Lists are spreadsheets with five fields used to record information from a publication's materials list. The Publication Taxon field is a free-text field used to record the name of a taxon used in the publication, and the Valid Taxon field is an ontology-enabled field linked to the Teleost Taxonomy Ontology, and used to record the current, valid name of the taxon. Comments or questions about a particular entry are recorded in the Taxon Comments column. Specimen information (museum vouchers) for each species is recorded in the Specimens table.
You can sort the data by clicking on any column header. Sort the "Taxon Comments" column to view the questions or comments that a student recorded about the taxon list. Also sort by "Valid Taxon" to view missing entries.
Making updates to taxon entries
If an author has made an error in the generic assignment of a species, which does not representing a difference in taxonomic opinion or concepts, then the current valid name of that species should be chosen, and add a comment in the Taxon Comments about your change. If you make any updates on a file or submit term requests for an entry, be sure to write a dated note in the Taxon Comments column detailing your actions (and preserve any previous notes left by a student).
Taxonomy ontology change requests
- Taxon name misspelled: Misspellings are requested as synonyms of the correctly spelled taxon name in the TTO. Choose the appropriate name from the Valid Taxon field, and add note in Taxon Comments field (e.g., Requested addition of synonym to TTO, Your Name, 7/28/2008)
- Taxon name not found: If the missing taxon name is a synonym of a valid name, then the synonym will need to be added to the taxonomy ontology. Add a note in Taxon Comments field (e.g., taxon XY is synonym of XZ: submitted TTO request on 7/28/2008 by Your Name). Leave the Valid Taxon field blank.
- Unnamed or unknown species: Examples of unnamed or unknown species in a Materials list might include: Danio sp., Cyprinus sp. 1, Cyprinus sp. 2, Danio aff. dangila, Danio cf. dangila, etc... These names should be added to the taxonomy ontology with reference to the publication. In this example, for a publication by Smith 2008, the request for new species names would be:
- Danio sp. (Smith 2008)
- Cyprinus sp. 1 (Smith 2008)
- Cyprinus sp. 2 (Smith 2008)
- Danio aff. dangila (Smith 2008)
- Danio cf. dangila (Smith 2008)
You need only submit one request per publication. See term request instructions for the TTO.
Museum Code Requests
We use the Fish Collection Codes spreadsheet on Google Docs, along with the taxonomy term tracker, to request the addition of missing codes, or request addition of synonyms of an existing code. See instructions here
Copy the updated taxon list to the folder named "old lists now updated by TTO requests" on Phenoscape fileshare.
Update entry for publication on Google Docs
Remember to make a note (dated) in the Taxon List Notes column of the shared publication spreadsheet on Google Docs (ask a PhenoScaper for access to the spreadsheet), recording that you have reviewed the taxon list and made any necessary term requests.