Diversity Taxon Names

External databases

Most names in DiversityTaxonNames were imported from external sources. These sources are documented in the area External data sources.

To enter or delete an external datasource, use the and button button respectively. With the button you will get a detailed information about the external database. For a valid URI you can use the button to open the corresponding website in a separate window.

To edit the datasources themselve, choose TaxonNameExternalID and TaxonNameExternalDatabase

Diversity Taxon Names

Hierarchy

The taxonomy for the choosen name is depicted in the area Hierarchy. If the taxonomy has not been specified a button set hierarchy will be visible

click on it to insert a dataset for the hierarchy of this taxon.

To choose a higher taxon you first have to specify the taxonomic rank of the choosen name

and type at least 2 characters of the higher taxon in the ‘Superior taxon:’ field.

Click on the drop down button ▼ to get the list of taxa above the rank of the name for which you want to set the hierarchy. The hierarchy will then be shown in the tree view (see below). The taxa below the current taxon will be displayed in gray.

The first line shows the taxon or taxonomic group superior to the choosen taxon. To directly access the database entry of a higher taxon, choose this taxon in the hierarchy tree and click on . The button  will delete this entry. As an alternative to delete the entry for the hierarchy, you may set it on Ignore to keep the information but exclude it from the creation of a hierarchical tree (see chapter Ignoreddata for further details). To get an overview of the whole hierarchy click on the button . You get an overview for the whole taxonomy including the current taxon as shown below. The line above the hierarchy tree shows the cached value for the hierarchy. After changes in the hierarchy this cached value may differ from the actual hierarchy. To refresh it, click on the button.

In the taxon tree the main taxonomic groups are indicated with icons (S = species, G = Genus, F = Family, O = Order, C = Class, K = Kingdom). To change the position of a taxon within the hierarchy, use the drag & drop function of the tree.

To enable a search within the hierarchy, please use the maintenace function to update the hierachy cache. The hierarchy is stored in one string, so to search for e.g. all members of e.g. a certain familiy e.g. Rosaceae, please use the ~ operator and a leading wildcard in your search string e.g. “% Rosaceae” or “* Rosaceae”.

The information about the hierarchy is related to opinions of the editors and are allways restricted to a certain project. The data of the hierarchy are stored in table TaxonHierarchy.

Diversity Taxon Names

List view

To see the data in a spreadsheet, choose View → List view … from the menu. A window will open where all names from the query will be listed.

Customize visibility of fields

To change the selection of the visible fields, click on the Column visibility button. A window as shown below will open, where you can change the visibility of the columns.

Customize sequence

To change the sequence of the columns, just use your mouse to drag the columns to the position of your choice.

Sorting of the data

To sort the data in the grid just click in the header of the column which you want to use as sorting column. The sorting sequence will be kept even if you change values in this column. That means that if you change a value in the sorting column the changed dataset will be placed at the new position according to its new value. The sorting of a column will be indicated with an arrow for the direction of the sorting (up or down).   

Change to data in main form

To change to a name in the main form, click on the , use the button. 

Formatting the grid

To adapt the width of the columns or the height of the rows either drag the border with the mouse, double click the border to get the optimal size for one column or respectively or click on the button for an optimal height of the rows or the button for an optimal width of the columns.

Exporting data

For an introduction see the video:

After setting the form according to your preferences, you can export the data with a click on the button. If the data should be appended in an existing file, change the option for the file handling from (= New file) to (= Append). The botton opens the folder containing the exported file.

Diversity Taxon Names

Projects

Projects with the DiversityWorkbench are located in the database DiversityProjects. The access to the data is organized via projects. The projects a user has access to can be selected in the query options.

To edit the project list use the project area. Use the  and  buttons to add or delete projects from the list.

If there are projects, to which you have no access, an additional list will appear, showing these projects (see below).

The information related to opinions of the editors are allways restricted to a certain project (see Database.).

Diversity Taxon Names

References

References related to a taxon can be added in the area “References”. Use the (add) and the (remove) buttons to handle the references.

The data of the references are stored in table TaxonNameReference.

Diversity Taxon Names

Relations

Relations between a taxa can be added in the area Relation. Use the (add) and the (remove) buttons to handle the relations.

The data of the relations are stored in table TaxonNameRelation.

Diversity Taxon Names

Synonymy

Basionym

The name on which the choosen name is based on should be entered in the “Based on:” field.

A name can be either an accepted name or a synonym to an accepted name. If nothing was specified so far, two buttons are visible:

choose one of these to make the choosen name to either an accepted name or a synonym.

Synonym

If the name is a synonym, the area for the synonymy will appear as shown in the images<

A name in most cases is synonym to one name but may sometimes be synonym to several names (e.g. pro parte). If you want to keep information of the synonymy you can set it to ignore (see chapter Ignored data for further details).

Delete a synonym

To delete a synonym, choose it in the list and click on the delete button .

Accepted Name

If the name is accepted, the form will show data related to accepted names

You can indicate accepted names in the search result list (in the menu choose View, indicate accepted names)

Conflict (Name declared a synonym and a basionym)

If by any chance (e.g. after import of synonymy relations from a foreign source) a name happens to be a synonym and an accepted name at the same time this is regarded as an error and will be shown as in the image below.

The data for the synonym are shown on the right side with blue labels, while the data for the accepted name are shown on the left with green labels. To correct this error you can either remove or ignore (see chapter Ignoreddata for further details) the assignement as a synonym or an accepted name.

Overview

In the area Synonymy overview you see the accepted name for the name you chose and a list of all the synonyms to this name. The sign  ≡ in front of a name following the accepted name means that this and the following names are homotypic synonyms to the accepted name. Groups of hetereotypic names start with a = in front of the first entry. If present, the first entry in each group is the basionym of this group. Names with unclear relation to the accepted name are preceeded by a “-”. To change to one of the names in the list, choose it in the list and click on the search button . The overview can be shown either as a list, corresponding to lists in publications or as a tree view. Use the  and  button to change between these views. In the tree view the current name is marked with a yellow background as shown below. The scrutiny of the search can be adapted by changing the number in the tool bar 3. As standard it is set on 3, but can be changed to values between 0 (just the current name) to 9. The higher the scrutiny the more thoroughly the search for synonyms will be performed and the longer it will take. To speed up the retrieval of the synonymy the results can be stored in a cache table as explained in the tutorial . Use the button next to the basionym to update the synonymy in the cache table for the current name or choose Administation - Refresh SynonymyListCache from the menu to update the content for all taxa in the database.

Explanation of the example above:

Editor

For a direct editing of synonymy list click on the button  . The list with the selected names and the synonymy overview will get a yellow background (see image).

Now you can add synonyms to the synonymy list by simply dragging them from the selected names list on a name in the synonymy tree view. If you drag the name on the accepted name, it will become a homotypic synonym of the accepted name. If you drag it on a heterotypic synonym, it will become a heterotypic synonym of the accepted name and get the same basionym as the name you dragged it upon. If this name has no basionym, the dragged name will become a homotypic name of the name you dragged it upon. If you want to create a new heterotypic synonym or a synonym with unknown relation to the accepted name, drag the name in the empty space of the tree view.

If you want to correct the synonymy you can drag the names within the synonymy overview either on another name to create a homotypic synonym or into the free space underneath the names to create a heterotypic synonym to the accepted name.

To remove a name from the lists of synonyms, choose it in the tree view and click on the button.

Isonyms, duplicates and orthographic variants

Some names are a variant spelled exactly as another name but with deviating citation of the author(s). These might be a name with wrong citation of the publishing or recombining author(s) or an isonym sensu ICBN. To change the type of the synonymy to an isonym choose the taxon and change the syn. type e.g. to “isonym”. In the synonymy overview list the isonyms, duplicates etc. are indicated by square brackets “[duplicate: … ]”.

Ignored datasets

If it should happen, that a dataset that is ignored is included in a synonymy in the form that another name is referring to this ignored name, the system will not be able to generate the synonymy properly. To detect ignored datasets in the synonymy choose “Query → Show ignored data” from the menu (see chapter Ignored data for further details). Ignored dataset will than be shown with red letters in the synonymy as shown below.

The information about the synonymy is related to opinions of the editors and are allways restricted to a certain project. The data of the synonymy are stored in table TaxonSynonymy. The data of the accepted names are stored in table TaxonAcceptedName.

Diversity Taxon Names

Lists for taxonomic names

With DiversityTaxonNames you can document list for taxonomic names like e.g. checklists. The taxon lists may refers to a project defined in DiversityProjects (see Administration - User … in the menu). To edit the taxon lists choose Administration → Taxon lists … from the menu. A window as shown below will open, where you can enter, edit or delete taxon lists. The administrative functions are only available for administrators. 

For the detailed documentation of the Taxon lists please use DiversityProjects. To load projects into the list, click on the Download projects from DiversityProjects button (see above). A window as shown below will open. If several Databases for DiversityProjects are available on your server you have to choose one of these. The projects available in the DiversityProjects database will be listed as shown below where those already present are checked and green, while missing projects are red. Check those projects you need as lists and click the Start download button.  

For access to the related data choose the tab Taxon lists (see below).  

To enter a new list, click on the button. This will open a window where you can choose from the available taxon lists. Choose the list in which you want to include your name and click OK.

Area

The geographical area can be definded for a single name (via Distribution) or for the whole taxon list. The entries refer to the World geographical scheme for recoding plantdistributions. To enter the geographic area for the whole list, click on the button. A form will open where you can choose geographical places from the module DiversityGazetteer. To open the link to the module, click on the button and search for the region as described in the chapter Module related entry.

If you need a certain region not provided in the list, just type the name of the region and click OK. The new region will be listed directly underneath the list (see below).

References

For every name in a taxon list, you can enter the references where the informations for the list are derived from. To add a reference, select the list for which you want to add a reference and click on the button. The entry for the reference will appear underneath the taxon as shown below. To edit this entry, select it in the hierarchy and use the contols underneath the tree. You may link the reference to an external source like DiversityReferences or one of the provided webservices.

If you want to transfer the informations of a reference together with depending analysis and distribution entries to another name, select the reference in the tree und click on the button. As a result you can use the button to insert these informations at a different place.

Analysis

For a name within a list, you can enter an analysis either directly for the name or a reference linked to this name. Select the name or the reference in the tree and click on the  button to enter a new analysis. Depending on the definition of the analysis To edit the analysis used within the database, select it in the tree and use the area below the the tree. Depending on the definition of the analysis (see above) the values are either typed or selected from a list.

To prevent a analysis from publication e.g. via the cache database in DiversityCollection, enter a withholding reason in the corresponding field . The sorting in an interface is set via the sorting. To check the current sorting click on the button.

Distribution

For every entry in a taxon list, you can document the distribution of a taxon (see below). This information may be linked to the taxon or a reference (see below).

Choose either the list taxon or the reference in the tree and click on the  button to insert a new distribution. The entries refer to the World geographical scheme for recoding plantdistributions. A form will open where you can choose geographical places from the module DiversityGazetteer. To open the link to the module, click on the button and search for the region as described in the chapter Module related entry.

If you need a certain region not provided in the list, just type the name of the region and click OK.

Specimen

For every entry in a taxon list, you can document the collection specimen linked to this taxonomic name (see below). The entries may be linked to the module DiversityCollection. To enter a distribution for the specimen, use the button. A window will open (see above), where you can select a geographic region as defined in the  World geographical scheme for recoding plant distributions. 

Export

To export the taxon lists resp. checklist, choose Data → Export taxon list … from the menu. A window as shown below will open. By default the data will be exported as XML (see below). Choose a schema file of your choice to convert the XML-output in a HTML document. You have several options for the export in regard of the names as shown in the window below. The export may be based on the names in the list and can be restricted to the accepted names among these (see below - left). In the second option (see below - right), the accepted names for all names in the list will be selected and the taxon list will contain only these names and optionally their synonyms. Regarding the synonyms, if you want to suppress the export of isonyms and duplicates, use the according checkbox. For long lists, the second method will be rather time consuming, as the synonymy must be checked for every single name. The synonymy for the exort may be derived from any available project. The path of the exported file (either *.xml or *.html) is shown in the field Export file at the bottom of the form. The names in the list may be sorted according to the names or the synonymy where synonyms will be inserted after their assigned accepted names. The format the XML-export with a schema file of your choice, choose the schema file and click on the button.

The tables involved in the storage for the taxon list are documented in the taxon list tables part.

Diversity Taxon Names

Edit Taxa In List

To edit the taxa in a spreadsheet, choose View → Edit taxa in list … from the menu. A window will open where all names from the query will be listed.

Customize visibility of fields

To change the selection of the visible fields, click on the Column visibility button. A window as shown below will open, where you can change the visibility of the columns.

Customize sequence

To change the sequence of the columns, just use your mouse to drag the columns to the position of your choice.

Sorting of the data

To sort the data in the grid just click in the header of the column which you want to use as sorting column. The sorting sequence will be kept even if you change values in this column. That means that if you change a value in the sorting column the changed dataset will be placed at the new position according to its new value. The sorting of a column will be indicated with an arrow for the direction of the sorting (up or down).   

Change to data in main form

To change to a name in the main form, click on the , use the button. 

Formatting the grid

To adapt the width of the columns or the height of the rows either drag the border with the mouse, double click the border to get the optimal size for one column or respectively or click on the button for an optimal height of the rows or the button for an optimal width of the columns.

Diversity Taxon Names

Data

To save the changes in a dataset click on the button.

To undo the changes in a dataset click the button. This will recover the original data unless the changes had been saved or changes were done in the synonymy.

To create a new entry in the database, click on the  button above the search result listbox. A window will open where you can add additional projects to the list in which the new name shoul be included (see below). By default only your current project will be selected.

Leave only those projects the new name is related to. Click OK to create a entry with the name “New Taxon”.

To copy a taxon, choose it from the list and click on the button . As with the creation of a new dataset you can insert the copy of a name into other projects (see above).

To delete a dataset click on the button .

Diversity Taxon Names

Taxonomic Name

The header shows the name, the ID and the version of the name - these data can not be edited. If a dataset should be ignored, check the checkbox “Ignore”. In the last field you can enter a revision level for the dataset. If you want to inspect the history of a dataset click on the  button.

Data concering the taxonomic name including the authors are entered in the corresponding area (see image below).

Depending on the taxonomic rank, the form will show only the fields available for this rank.

If the genus is linked to an entry in the database, the field for the genus will change as shown here and the program will not allow you to edit the name. To edit the genus of the name, click the button to release the link to the genus. The list of genera is restricted to the project you selected. If a hierarchy is availble for the selected genus the hierarchy will be automatically inserted for the current name.

If the name is a hybrid , check the checkbox “Is hybrid” to get access to the fields for hybridization.

Diversity Taxon Names

Authors

For names according to an official code (ICBN) the authors of the name should be given.

To edit the authors using standard abbreviation list click on the Button. This will open the form for editing the authors.

here you add (click on the button) and remove (click on the button) authors according to the standard list. You can choose the standards for the abbreviation from the provided lists.

For names not following an official code authors should not be given. Instead, include a descriptive phrase in the field Non nomenclatural name suffix.

To edit the selected list of the authors click on the Edit author list button.

Diversity Taxon Names

Nomenclature

DiversityTaxonNames was developed to follow, for the most part, the International Code of Botanical Names (ICBN). Other codes like the code for names in zoology have not yet been taken into account. Information corresponding the nomenclature are entered in the provided fields as shown below.

Diversity Taxon Names

Taxonomic reference and protologue

Details about the protologue are entered in the area Taxonomic reference / Protologue

To enter a website for the protologue either enter the link in the field or click on the button to start a query. This will open simple browser where you can search the URL for the protologue as shown below.

Diversity Taxon Names

Typification

Details about the type can be entered in the area “Typification”.

The navigate through the data use the , , and button. To add a new typification use the button, to delete the current dataset, use the button.

Diversity Taxon Names

Hybrids

As for the time being a definite rule for the creation of a valid taxonomic name on the basis of the parent names is not available. Therefore the name is build from the genus and all the rest placed in the field for the epithet. Some examples for hybrids are: 

• Asplenium x alternifolium Wulfen.
• Coeloglossum x Dactylorhiza Coeloglossum viride x Dactylorhiza majalis subsp. praetermissa
• Ononis repens subsp. procurrens x spinosa subsp. spinosa
• Salix (caprea x viminalis) x (purpurea x viminalis)
• Salix alba var. vitellina x babylonica x matsudana
• Symphoricarpos albus var. laevigatus x microphyllus x orbiculatus

As soon as a rule is available the name can be generated from the parent names that are entered as described below.

If a taxon is a hybrid, check the checkbox to open the part for the entry for the parents of the hybrid. You can determine up to 4 parents for a hybrid as shown in the figure below

Diversity Taxon Names

Common names

A name can have several common names. These are entered in the section Common names. To add or delete a common name use the  and  buttons.

The data of the common names are stored in table TaxonCommonName.

Diversity Taxon Names

Ignored Data

To remove data from the creation of the hierarchy, the synonymy etc. on one hand and not to delete them but to keep the information, use the Ignore option. All data set to Ignore are no longer involved in the normal queries, but kept to ensure e.g. links from other modules. To display ignored data, select Query - Show ignored data in the menu.

Synonyms

In the example below, a synonym was set on ignore.

If it should happen, that a ignored name is included in a synonymy and a name within the synonymy is referring to this ignored name, the system will not be able to generate the synonymy properly. Ignored names will than be shown with red letters in the synonymy overview as shown below.

Accepted names

In the example below, the entry for an accepted name was set to ignore, now showing this information side by side with the current setting of the name as a synonym.

If several entries for an accepted name exist, a list will appear at the left side as shown below where to top entry (0) is the valid entry, while all other entries (> 0) are set to ignore (see below).

Hierarchy

As with the accepted names, ignored data will be listed as shown below in a list where to top entry (0) is the valid entry, while all other entries (> 0) are set to ignore. 

Diversity Taxon Names

Geography

Details about the type can be entered in the area “Geography”.

The geographical distribution of the type specimen according to the protologue can be typed in the field Locality of the area Typification. In the area Geography names according to a standard can be entered as a list as shown above. To remove an entry from the list click on the button. To add an entry click on the button. A form will open where you can choose geographical places from the module DiversityGazetteer. To open the link to the module, click on the  button and search for the region as described in the chapter Module relatedentry.

The data of the geography are stored in table TaxonGeography.

Diversity Taxon Names

Resources

Resources related to a taxon can be added in the area “Resources”. Use the (add), (remove) and (save) buttons to handle the resources.

Resources are sorted by their order which can be set in the field shown below. If a resource should not be published, enter any text in the field. The title will be shown e.g. in a chart query in the tooltip of the image.

The data of the resources are stored in table TaxonNameResource.