Handling taxonomy

Page in Finnish: Taksonomian hallinta

Managing taxonomy is mainly outsourced to a separate system, FinBIF Taxon editor. It takes care of checklists, taxonomic hierarchy, synonyms etc.

Connection to taxon database (situation 10/2021)

Kotka has been connected to taxon database in the following ways:

Data entry

When you start typing a taxon name to the Taxon name field on Kotka web form, it suggests matching taxon names as a dropdown (screen capture). Taxon names are fetched from the FinBIF master checklist in taxon database. When one of the suggested names on the list is chosen, taxon rank and author are filled in automatically. In Excel templates these need to be entered manually.

If you type the taxon name, rank and author completely, Kotka checks whether the combination is found in master checklist and gives a warning if it is not found (screen capture). It is still possible to enter any taxon names, also those that are not found.

Specimen view

If the name is found in the master checklist, Kotka fetches the accepted taxon name and to the specimen information (specimen view). It is also possible to print the accepted name to labels.

Specimen search

In specimen search,the field Taxa includes taxon hierarchy above the recorded level (family, order... all the way to Biota), if the taxon is found in the taxonomy database.

Specimens can be searched based on the accepted name, the taxon hierarchy, family and synonym names (fields AcceptedTaxon, Taxa, Family and Synonyms, respectively) in search. There are still some issues with synonym search (10/2021). Specimens can also be searched based on the taxon's conservation status (search field endangeredStatus). If a specimen has a taxon name that is not found in the master checklist, it can only be searched using the exact name that was typed for it (in Kotka and laji.fi). When new names and checklists are added to the taxon editor, the changes will be updated to Kotka the following night.

Example

Specimen http://id.luomus.fi/KS.1 has been entered to Kotka using the name "Psetta maxima" and author "(Linnaeus)". In taxon database this is a synonym for the species "Scophthalmus maximus (Linnaeus, 1758)". Both names are shown in specimen viewer in Kotka.

Taxon hierarchy can be viewed in the specimen search result table in the field Taxa.

Garden Accessions

For garden accessions view page, taxon name is shown on the top of the view, and it functions as a link to the taxon card, if the taxon is found in taxon database.

Known issues

• Kotka suggests also names below species level to taxon name, but these can't be entered to Kotka in one field, they need to be separated to their own fields. This is related to the feature that taxon database only has one field for the entire taxon name and Kotka has multiple.
• Taxon database contains mostly data on only Finnish species, so when entering data on foreign specimens, there is no linkage to taxon database.