Maintenance - Taxonomic names

Taxonomic names may be linked to an external source. To synchronize the entries for the taxonomic names derived from the module DiversityTaxonNames choose Administration -> Maintenance... from the menu. A window will open as shown below. Choose the tab TaxonNames. There are two ways to synchronize taxonomic names. You may either Synchronize taxonomic names based on the link via an URI for entries where the link to a taxonomic database is already established or you may Synchronize taxonomic names missing a connection where no link is established and you can query for identical names in one of the databases.

Synchronize taxonomic names based on the link via an URI

The taxonomic names are stored in the field TaxonomicName in the table Identification. Select a taxonomic database and a project and taxonomic group which should be synchronized. Start the query with a click on the Check for differences button.


If the taxonomic information has been imported into the cache database, you may use the data from there to speed up the synchronization.

The form will list all differences found. With the Select same genus and species button you can restrict the selected entries to those where the genus and species are identical in the source and the entry in collection. The other buttons will either select all or no entry .

To update the database click on the Start update button. If you wish to have a more detailed look on your data, you need to check the Include accession number checkbox before starting the query. A button Close form and check dataset in database will appear which will take you back to a single data set in the database.


Synchronize taxonomic names missing a connection

Select a taxonomic database and a project within this database, a project in the collection database and a taxonomic group to search for identical names. Start the query with a click on the Check for identical names button. You have several options to search for fitting names:

Compare whole name

Search for an exact match. With the option Excl. auth. you can extend the search for names where the authors are missing in the identifications.

Compare first parts

Search for names fitting in first parts of the name as shown below. If the names do not match exactly, you may either update the name ( Update similar name) in the collection database or import the name from the DiversityTaxonNames as a new identification ( Insert as new name - see options in the window depicted below).

If you choose the option Restrict to last identification, the former identifications of an organism will be ignored.

If you choose the option Include fuzzy search, the program will try to find names with up to 3 differences. The search with this option is rather time consuming and should only be used for a small number of datasets.

In the result list only matching names will be checked (column OK). The other results will be marked indicating the difference.

If several similar names were found, these lines will be marked with a blue background. To select one of the similar names click on the Select valid name button. A window will open as shown below listing all similar names found in Index Fungorum. Select one name and click OK to use it.


Search for broken links

If for any reason links to webservices or modules are broken, e.g. when a webservice changes its address, you can search for these (see below). Please make sure, that you are connected with all source databases used for the taxa. Otherwise connections to these sources would be assumed as broken. Choose the Project, for which you want to search for broken links and optional restrict the search on a Source and a Taxonomic group. Click on the button to start the search.

The broken links will be listed as shown below. With the Check dataset in database you can inspect a single dataset. With the Select all and Select none buttons you can select resp. deselect all datasets and show the selected datasets with the Close form and check whole list in the database button in the main window.



Update the display text for organisms according to last identification

If for any reason the displayed text for an organism does not correspond to the last identification, this can be fixed under the Synchronize last identification tab. Just click on the Search for organisms where the displayed text does not correspond to the last identification   button to list the deviating display text and then on the Update the displayed text for organisms according to the last identification button to synchronize the displayed text with the last identification.