Update Taxon Lists
If you need to create a taxon list for a publication, see Creating Taxon Lists instructions.
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.
As always, make sure to Update your project files using ZigVersion, then start up Phenex and open the relevant 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
The Taxa and Specimens Panels are used to record information from a publication's materials list. Within the Taxa Panel, the Publication Taxon field is a free-text field listing the names of all taxa 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 names of the taxa. Comments or questions about a particular entry are recorded in the Taxon Comments column. The Matrix Taxon field (which you usually do not need to edit) is used to record the name of taxa used in the matrix. 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
The names listed in the Publication Taxon column are those used in the publication, and should not require editing by curators (though edit if there is an obvious mismatch with the publication, usually because of a mistaken entry by a student). Valid Taxon names will usually need to be updated.
Not all publication taxa need to be updated with valid taxon names: only update those that were used in the matrix. To find taxa associated with matrix data, look at: 1) the Matrix Taxon column in the Taxa Panel, which will contain higher level taxon names if used by an author as a placeholder for multiple taxa; 2) the Publication Taxon column within the Matrix Panel (View > Annotation > Matrix).
If you make any updates on a file or submit term requests for an entry, be sure to write a note in the Taxon Comments column detailing your actions.
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)
- If an author has made an error in the generic assignment of a species, which does not represent a difference in taxonomic opinion or concepts, then the current valid name of that species should be chosen, and the erroneous name should be added to TTO as a synonym of the valid name. The curator should add a comment in the Taxon Comments about the request.
- 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).
- 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
Check In modified file to the data repository
After making your taxon update, save the file and return to ZigVersion. Select the top-level folder ("/") and click "Check In." Type a short comment explaining the changes made to the file, then click on the Check In button, and click "ok" within the Check In box that appears.
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.