Diversity Scientific Terms

Scope of DiversityScientificTerms within the Diversity Workbench

DiversityScientificTerms is part of the database framework Diversity Workbench. Within this framework the application DiversityScientificTerms is confined to the management of scientific terms. Any module within the Diversity Workbench is focused on a specific data domain. DiversityScientificTerms keeps only data connected with the handling of scientific terms. Data of other realms are handled in separate modules. For an overview of the available modules see the image below. The current version relies on the service of DiversityAgents for explicit information of users etc., on DiversityProjects for further informations about terminologies and DiversityReferences for explicit information about references. DiversityCollection is dependent upon DiversityScientificTerms to characterize terms.

Despite the connections to other modules of the Diversity Workbench DiversityScientificTerms may be used as a stand-alone application.

Diversity Scientific terms

Download

Upcoming version

4.2.1

SQL Server 2016

For this version you need SQL Server 2016 or higher

New table JsonCache containing the data related to a term as JSON. In the menu accessible via Administration → Json cache … or in the header click on the Show JsonCache button to see the json cache for the current term.

Current version

4.2 (2023-05-10)

Download

Bugfixes in Workbench.dll
Bugfix setting permissions
Database documentation: Enumeration tables with specific title and generic table definition

Previous versions

4.1.21 (2023-02-22)

Bugfix creating archive
Bugfix linking to client software site
Many order columns enabled
New order columns Property, Section, Resource, Reference Ranking hierarchy included
Docu: Bugfix retrieving column description for views

Database updates

01.00.15: New views View_TermProperty, View_SectionTerm, View_TermReference, View_TermResource, View_TermRankingHierarchy for query; Missing defaults for table TermDependency; Missing descriptions for tables, views, …; New function TerminologySize if missing; New column ArchiveProtocol in table Terminology including log table and trigger; Function TerminologyDataLastChanges; Missing grants for table TerminologyPropertyValue; Removing not used type - moved to table TermRepresentation;

Diversity Scientific terms

Installation

Resources

To run a module of the Diversity Workbench framework, you need access to a database and an installation of the respective client. The following instructions explain how to install the DiversityCollection client. All other modules are installed in the same way.

If you do not yet have an account for your institutional DWB platform, please contact your institution’s DWB administrator. If you wish to set up and use your own personal, institutional, domain-specific, or research-group-internal database environment, see Installation of a database for more information.

A German-language video demonstrates the installation using the DC client as an example. Please note that the initial steps in the video are outdated, as the downloads are now available via this manual, as described below. .

Download

All DiversityWorkbench modules can be downloaded free of charge. Within each module in the manual, you will find a Download menu item. There, you can download the latest version in the Current version section.

Installation of the client

The client is currently based on the .Net framework version 4.8 from Microsoft. If not already present, the software will prompt you to install it.

After downloading the client, unzip the .zip folder. The extracted setup folder contains two files: an .msi and a .bat file.

If you want to install the client on your computer, start the installation by double-clicking the .msi file.

If necessary, you can adjust the installation location in the next step.

Once the installation is complete, the software will be added to the program menu (see below) and a shortcut will be created on the desktop.

In the next chapter Database Login the login process is explained.

Troubleshooting

If you don’t have sufficient permissions on your computer to install anything, you can use the client by following the instructions Run the program without an installer. If you receive a warning from Windows that this computer is protected, follow the instructions Windows protection warning.

Run program without installer

There are several reasons why you might prefer to run DiversityCollection without installation. E.g. if you lack administrative permissions on your computer or if you want to use several different versions of DiversityCollection in parallel.

Therefore, the downloaded .zip file contains a .bat file. With this .bat file, a folder DiversityCollection_x_x_x is created on your desktop containing all relevant files to run the client DiversityCollection.

You have to unzip the downloaded .zip file to a local folder. The unzipped folder contains the .msi file and the .bat file. Within this unzipped! folder start the .bat file with a double-click. You might get a security warning, as shown in the section Windows protection warning.

The batch file unpacks the program files to a folder on your desktop named DiversityCollection_x_x_x, where "x_x_x" stands for the program version.

To start the DiversityCollection program, go to the folder and double-click on the file DiversityCollection.exe.

The login process is explained in the next chapter Database Login.

Technical notes and additional information

The software will be placed in the programs directory, as shown below.

Additionally, a folder is created in the user directory. This folder contains files and templates, for example, for label printing. It also contains hidden folders, such as Query. User input is saved there so that it can be loaded again the next time the program is started.

Windows protection warning

If you receive the following warning from Windows

please click on Weitere Informationen. A button Trotzdem ausführen will appear.

Please click on Trotzdem ausführen to install the software.

Diversity Scientific terms

To use a module from the DiversityWorkbench framework, such as “DiversityCollection”, you need access to a database. If you do not yet have an account for your institutional DWB platform, please contact your institution’s DWB administrator. If you wish to set up and use your own personal, institutional, domain-specific, or research-group-internal database environment, you will find instructions here.

Connect to a database

At the top left of the main window, go to Connection → Database … or click the Connect button . A dialog form “Connect to database” opens.
In the “Server” section, add the server name or the IP address and the port number.
In the “Login” section, choose an option:
- Windows authentication: Using the Windows Login information.
- SQL-Server authentication: User and password as defined in the database.
Click on the Connect to server button.
If the connection information is valid, you can Choose a database from the drop-down list at the bottom.
Choose the database you want to work with and click OK.
If you access a database for the first time, you will be asked to consent to the storage and processing of your personal data (see below) according to the General Data Protection Regulation. Without your consent the access is not possible.

Important The standard port number for SQL-Server is 1433 and is set as default. If the database server is configured to use a different port, you must change the port number in the port input field.

Previous connection

If you have been connected to a database in previous sessions, you can select one of these connections:

At the top of the “Connect to database” dialog form, click on the Previous connections button .
Select a connection from the drop-down list. This inserts the name or IP address and the port in the corresponding input fields in the server section.
To log into a database, proceed as described above starting from step 3.

Testing a connection

To test the connection, you can send a ping by clicking the button .

As a first step the IP resp. Server will be tested. If the connection to the server is successful, the port will be tested as a second step.

Switch between databases

At the top left, go to Connection → Database … or click on the Connect button .
If you are already connected to a server, you can select a database from the drop-down list Choose database at the bottom of the dialog box.

Reset and Cancel

Reset: If you are connected to a server, there is a Reset button below the “Login” section of the “Connect to database” dialogue box. Click the Reset button to change your server or login settings.

Cancel: If you do not want to change anything, click on Cancel.

Encryption

By default, the connection to the databases is encrypted. The icon next to the Connect to server button indicates an encrypted connection. By clicking on the icon, you can switch to an unencrypted connection, indicated by the icon .

Videos

Diversity Scientific terms

Overview of the menu in DiversityScientificTerms

Connection
- Database Choose one of the databases available on the server. Only those databases will be listed to which the user has access permission..png?class=inlineimg)
- Module connections … Edit the connections to the other modules within the DiversityWorkbench.
- Transfer previous settings Transfer the settings of a previous version.
- Quit Quit the application and stop all processes started by the application.
Data
- Table editors Edit data as selected in the query data directly in the data tables.
  - Term … Edit data of the Term table.
  - Representation … Edit data of the TermRepresentation table.
  - Property … Edit data of the TermProperty table.
  - Reference … Edit data of the TermReference table.
  - Resource … Edit data of the TermResource table.
- Backup database … Backup of the whole database
- CSV (bcp) Export data of the whole database as csv files
Administration
- Database Administration of the database
- Documentation … Documentation of the tables within the database
- Logins … Administration of the logins of the server their permissions in the databases
- Rename database Rename the current database
- Set published address Setting the address published for links by other modules
- Database tools … Creation of log tables, triggers etc. (only for dbo)
- Language … Enabling languages for the terms.
- Resources directory … Setting the directory for the resources.
- Terminologies … Administration of the terminologies.
Help
- Manual Opens the online manual - Info Show the version and corresponding information
- Feedback … Opens a form for sending feedback
- Feedback history … Opens a window for browsing former feedback.
- Edit feedback … Opens a window for editing the feedbacks sent to the administrator (for admins only).
- Websites Websites related to DiversityScientificTerms
- Download applications … Download DiversityScientificTerms from the website of the Diveristy Workbench project
- Information model … Inspect the information model on the website of the Diveristy Workbench project
- Errorlog Inspect the errorlog of DiversityScientificTerms
Update
- Update database … Update the database to the current version
- Update client … Download the current version of the client

Diversity Scientific terms

Query

Once you are connected to your database, you can search across all data. A wide range of search options is available.

All functions related to querying can be found on the left-hand side of the main window.

The upper part of the query section contains the list of all results, titled “Query Results”.

Below this, you will find a section containing all the buttons relevant to the search.

Below the query buttons, you will find the “Query Conditions” section. This is where you can enter all available search criteria.

Perform a Query

Display the Entire Dataset

To display the entire dataset, start a search without specifying any criteria in the “Query conditions” section:

In the middle of the query section on the left-hand side of the main window, click on the “Filter” button.
A list of the results will be displayed in the “Query Results” section. The number of results is shown above the list, next to the “Query Results” label.

Filter a Search

Below the query buttons, at the bottom of the query section, you will find the “Query Conditions”.

Enter the filter criteria for your search. For example, you can select a project from the dropdown list.
You can combine as many criteria as needed to narrow down your results.
Start the query by clicking the “Filter” button .
A list of results will be displayed in the “Query Results” section. The number of results is shown above the list, next to the “Query Results” label. If no results match the query, the list remains empty and the label “No match” is displayed.

Edit and Customise Query Conditions

You can choose which query conditions are displayed in the main window, and you can change this at any time.

At the top left, above the query results list, click the “Checkbox” button .

Select any query conditions you want to use for your searches by selecting the respective checkboxes in the treeview.

Customise the Interface

Hide/Show the Entire Query Section

In the main window, go to the menu item Query → Show Query.

Hide the “Query Conditions” Section

On the left side of the “Query Buttons”, in the middle of the query section, click the “Arrow” button .

Switch Between Vertical and Horizontal Arrangement

You can change the layout of the query elements from vertical to horizontal and vice versa. To do this, click the button located below the main menu bar:

Edit the Result List

Add Results to the Existing List

You can add new results, based on different query conditions, to your current result list.

Enter the new filter criteria for your additional search.
Start the query and add the results to the existing list by clicking the button .
The new results will be appended to the existing list.

Remove Result Items from the List

You can remove entries from your current result list:

Select the entries you want to remove.
Click the button .

Important This does not delete the data from the database. It only affects the current display in the results list.

Many Result Columns

The option to display a result list with many columns is described in the chapter Many Columns.

Query Conditions

Remember the Last Query

By default, the values you entered for the previous query will be remembered. Your query criteria will be pre-filled when the programme starts. To change this behaviour, click the Pin button .

Query Annotation

The query for annotations differs from a standard query (see below). In addition, you can specify the type of annotation (Annotation , Problem , Reference ) and the linked table (see Annotation).

Duplicates

Certain query condition fields allow you to add up to three duplicates of the same condition. For adding a ‘duplicate’ search criteria, click the green “Plus” button . Remove a ‘duplicate’ search condition with a click on the red “Minus” button . The restrictions can be combined with AND + and OR |. To switch between these modes, click the resp. + or | icon.

Query Modules

In the “Query Conditions” section, some values may be linked to other modules. For example, within the “Identification” group, the fields “Taxa” and “Terms” are linked to the “DiversityTaxonNames” and “DiversityScientificTerms” modules, respectively. You can also add “linked” values to your query condition.

Select the operator that determines how the entries are used in the search. An explanation of all available operators can be found in the table below.
To connect to the linked module, click the “Ammonite” button located to the right of the relevant query field.

A query window for the linked module will open.
Search for values within the linked module and click “Ok” to confirm your section.
If you want to view a list of the selected items, click the Magnifying Glass button .

Info: There is also a detailed available, which explains all possible operators and how to use them.

Operator	Meaning	Example
∈	Search for entries with a list	Rosa \| Rosa caninia \
∉	Search for entries not within a list	Rosa \| Rosa caninia \| ...
+H	search for entry including lower hierarchy	Picea \| Picea abies \| ...
+S	search for entry including synonyms	Picea abies \| Pinus abies \| ...
+HS	search for entry including lower hierarchy and synonyms	Picea \| Picea abies \| Pinus abies \| ...
	Change filter mode between link and text	http://tnt.diversityworkbench.de/TaxonNames_Plants/4269 <> Picea abies L.

Query any fields

The query for any fields will search in several fields, e.g., withholding reasons in specimens, images, etc. There are two versions: The first version (e.g., Notes) will search in all tables but not in collection event tables, while the second version (e.g,. Any notes) will search in any table (see image below).

Videos

Introduction on how to use the query conditions:
How to use special query conditions:
Tutorial on how to query modules:
Tutorial on how to save a query: .

Wildcards in SQL

There are 4 different possibilities for wildcards in SQL:

Operator	Description	Example	Result
%	any string consisting of no, one or many characters	Pinus %	will find anything like Pinus, Pinus sylvestris, Pinus strobus etc.
*	same effect as % (see above)
_	a single character	Pinus s_lvestris	will find Pinus sylvestris and Pinus silvestris etc.
[…]	any character out of a given range like [abcde] or [a-e]	Pinus s[iy]lvestris	will find Pinus sylvestris and Pinus silvestris
[^…]	any character not in a given range like [^abcde] or [^a-e]	Pinus s[^i]lvestris	will find Pinus sylvestris but not Pinus silvestris

Many colunns

The option to include several columns in the result list is only available for optimized queries . To display several columns in the result list, click on the button next to the order by column (see below). A window will open where you can select the next column for the sorting. Underneath the order by column the second column for the sorting will be added. To remove this sorting column you can click on the button. By default the width for the columns is set to 10. You can change this according to content. To set the width to the maximal length of the current content, click on the button. To change the sorting of the added order column click on the button. The colums are separated via " | " as shown in the image below.

For an introduction see the videos:

Mehrspaltige Suche:
Sortierung:

Diversity Scientific terms

Editing the data

The main form of DiversityScientificTerms contains two main areas. On the left you find the query and the results of this query. On the right part the details of a dataset selected in the result list is shown. The upper part of the data area shows the position of the current term within the hierarchy. In the lower part you find the fields for the details of a term. At the base of the window the properties, references and resources of a term are listed.

For every term one representation can be set the preferred one, indicated by the icon. To make a representation the preferred representation, simply click on this icon.

Display settings for charts etc.

For display in an interface used from other modules like DiversityCollection, e.g. via a chart, a term may have a display order, a color for the background and an image.

The display order will be applied within the terms of the same hierarchy level and works top down, so the term with the lowest display order will be presented at the top of the list.

To set the display color, click on the set color button. A window will open where you can either select an available color or define a new one. The color will e.g. be used as background in a chart. If depending terms should use a color of the same hue, click on the button to activate the inheritance for the color. The button will change to . See chapter chart for details.

To set the display image for a term, click on the button. A window will open where you can search for the image that should be presented. In a chart, the size of the image will be scaled down to a maximal width of 100. To remove an image, use the button next to the image.

After editing the data, click on the button to save your data. To see the description of the fields, just move the mouse into it. A small window will appear, showing the description. To see the description of all fields turn to the description of thedatabase.

Copy data

To create a new term click on the button above the query list. A form as shown below will open where you can enter some basic informations for the new term.

To create a copy of a term, choose an entry in the query list and click on the button besides the hierarchy. A form as shown below will open providing you with the possibility to create a synonym, an inferior dataset or a copy on the same level in the hierarchy as the original dataset.

To create a synonym of a term, choose an entry in the query list and click on the button besides the hierarchy. This will create a synonym to the original dataset.

To make a term a synonym to another term, choose the term in the hierarchy and click on the button besides the hierarchy. This will open a window, where you can select the term to which the current term should become a synonym to.

To delete a dataset, select it an click on the button.

Diversity Scientific terms

Chart

The module DiversityScientificTerms provides other modules the option to query the terms on basis of a chart. These charts are created on basis of the selected terminology or sections and in case there are sections available To test the chart of the current terminology, select Test - Chart from the menu. In case there are sections a window will open where you choose the data you want to show in the chart. A window as shown below will open. To test the chart, select an entry and click OK.

Ranking terms resp. types

The chart is not available for ranking terms resp. types .

Sections

Terminologies may contain sections. If no sections are available, only the whole terminology will be presented (see below).

If the terminology contains sections, you can choose either the whole terminology or a section. If you choose a section only the terms within the section will be shown and the name of the section is shown in the header (see below).

Images

If a term has images, these images will be shown in the chart as shown below. The images will be shown according to the order set for the images. If a title for an image has been defined, this will be shown in the tool tip when you moove the mouse above the image. If no title has been defined either the synonyms the term will be shown or if no synonyms are defined the display text of the term. The width of the images is restricted to 100 pixel, larger images will be adapted accordingly.

Colors

Every term may have display color . Click on the set color button to select a color for the term. This color will be shown as background for the term as shown below. If no color has been choosen, a greyscale value will be used as background as shown above.

If the terms depending on a term do not have a color of their own and the inheritance of the color is activated, a hue of the parent term will be used as shown in the image below. To activate the inheritance of the color, click on the button. It will change to and the color will be inherited to depending values as shown in the image below.

To select an item, click on it so the corresponding ID will appear in the box in the left upper corner. If there are synonyms available for a term these will be shown via a tooltip as shown below.

Files

The html files for the chart will be generated in the user directory as shown below. The file …_ChartSelect.html is the main file. the other files like e.g. …_ChartSelect_71_76.html are depending files that contain the items with the parent ID 71. These files will be removed when you close the chart.

The html files and the chart are adapted to the width of the window of your application, so if you change the width of your main window, the files will be regenerated to ensure that the displayed columns fit into the available space. In the examples below, the chart has been selected with two different widths that result in a regeneration of the files.

The html file below has been generated with a reduced with of the window with the links to subpages starting on a higher level. The fields with a colored background let you select the displayed items while the fields with a link lead you to a subpage containing depending items (e.g. Coastal dune and sand habitatas in the example below).

A field with a link will lead you to a subpage as shown below. The link at the top of the subpage will lead you back to the page where you came from (← Coastal habitatas in the example below).

Diversity Scientific terms

Dependency

For an introduction see the video:

The terms of a certain type/ranking may be dependent on terms that are no types/ranking, e.g. terms of the type Zement may only be available for terms underneath the term Sedimentgestein which itself is of the type Gestein. Clients that want to use any term of a dependent type (e.g. Zement) must therefore first insert a term of the type of these terms depend on (e.g. Sedimentgestein) or underneath in the hierarchy (e.g. Kalkgestein). The clients afterwards will contact the database including the information of the first term (e.g. Kalkgestein) and will in return get a list of all terms of which the type (e.g. Zement) is defined as dependent on the first term (e.g. Kalkgestein) resp. a parent of this term (e.g. Sedimentgestein). The image below shows the relationships in an example.

To define dependencies, change to Ranking terms (in the menu click on Ranking terms to switch to the administration of the types resp. ranking terms (see image below)). This part is only accessible for users in the group Editor or above.

Diversity Scientific terms

Hierarchy

The upper part of the form shows the term in the hierarchical relation. To insert a relation to a broader term, click no the button. In the window that will open, select the broader term from the list and click OK. To remove the relation to a broader term, click on the button. The image below summarizes the options to depict the relations in the hierarchy.

The default view of the hierarchy is shown below.

If you want to see the synonyms, click on the button. The button will change to and the hierarchy will show the synonyms with the indaction of the language. Synonyms of the current term will have a pink backgroud.

If you restrict the output in the hierarchy to a certain language, only one language will be shown in the hierarchy as shown below.

In the image above the hierarchy is restricted to the superior terms. If you want to see the whole hierarchy click on the button. It will change to and all terms will be shown. To return to the previous view, just click the button again.

A cached value of the hierarchy is stored in two fields (downward and upward) for every term. These entries are needed e.g. for queries where the whole hierarchy is used instead of the term itself. The hierarchies are build using the preferred terms (see Editing thedata ).

Diversity Scientific terms

History

To inspect the history of a dataset click on the button. A form will open, showing all former states of the data in the tables with the current dataset at the top.

Diversity Scientific terms

Language

To edit the language list available for the selection of the synonyms, choose Administration - Language from the menu. In the window that will appear, you can enanble or disable certain languages (see below). With a click on the Disable languages that are not used button, you can disable all languages that are not used for synonyms so far, which will shorten the list for selection in the main form..

Diversity Scientific terms

Properties

The properties that can be asigned for a term might be defined under the terminology to which the term belongs. To insert a new property, open the form Terminology. You find the properties defined for a terminology in the base part of the form as shown below.

The properties that are defined in the terminology are then available for a term. Depending on the datatype set for a property in the terminology, you can either enter list, text, numeric or date values for a property of a term as in the example above numeric values for an age. For properties of the datatype list, an area for the entry of the dedicated (text) values will appear as shown below.

The values for a term will be restricted to the list of values (see below).

Diversity Scientific terms

Ranking terms

Every term should be characterized by a ranking term or type. These ranking terms are edited in a separate list, not to be mixed up with the terms. To switch to the editing of the ranking terms, click on Ranking terms in the menu that will switch to Ranking terms and list the ranking terms (see image below).

If in the query for the terms Ranking has been selected as the display column, this will be changed to Display Text as Ranking is not available for Ranking terms. To edit the ranking terms / types a user needs to be in the group DiversityWorkbenchEditor or above. For the ranking terms, you can define a dependency from a term.

Diversity Scientific terms

References

For every terminoloy and every term you can insert references.

There are 3 options to enter a reference:


1	as simple text
	just enter the title of the reference in the text field as shown below

2	linked to a module like DiversityReferences or a webservice
	Click on the button to open a window where you can search and select for a reference in e.g. the module DiversityReferences. You need access to DiversityReferences or a corresponding webservice to use this option.

3	a URI of a website
	click on the button to open a browser where you can choose the reference from the web

The data are stored in the tables TermReference and TerminologyReference respectively.

Diversity Scientific terms

Resources

For every term you can insert resources, including informations about the creator, the license etc. (see image below). Use the and button to add or remove images. If an image should not be shown in an external user interface, e.g. in a chart in another modul like DiversityCollection, enter the reason in the field. The image will change to and the pink background will indicate the withholding of the image. The title will be shown as tooltip in a chart.

To see an image, click on the button. A window as shown below will open.

The data are stored in the tables TermResource.

Diversity Scientific terms

Sections

The sections that can be asigned for a term must be defined under the terminology to which the term belongs. To insert a new section, open the form Terminology. You find the sections defined for a terminology in the base part of the form as shown below.

The sections that are defined in the terminology are then available for a term. Choose the and button to add resp. remove a term from a section (see below). To Insert all Terms listed in the query results to a section, choose Data - Add to section from the menu.

Diversity Scientific terms

Synonyms

Every term may have several synonmys. The preferred synonym, shown in picklists and the like is marked with a green icon. To make another synonym the preferred icon, click on the button. To make a term a synonym to another term, click on the button. In the window that will open, select the synonym from the list and click OK.

To create a synonym of a term, choose an entry in the query list and click on the button besides the hierarchy. A window as shown below will open. Enter the display text and choose the language of the new synonym. This will create a synonym to the original dataset.

If you want to see the synonyms in the Hierarchy, click on the button. The button will change to and the hierarchy will show the synonyms with the indaction of the language. Synonyms of the current term will have a pink backgroud.

If there are several synonyms, the perferred term will be marked green while the other synonyms are marked pink. The current term will be marked yellow (see below).

Diversity Scientific terms

Table Editors

For the data selected in the main window the table editors offer a direct access to the tables of the database. The menu Data - Table editors provide an editor for Term… , Representation… and Resource…

A window with the content of the table will open. Columns with a gray background can not be edited here. Columns with a light gray background are linked to the contents of lookup tables where you can change according to the contents of these tables.

Select Set timeout … from the menu to increase the default timeout from 5 seconds to a higher value, e.g. for greater amounts of data.

Editing

You can either edit the contents of the table directly or perform changes to any number of marked fields. To mark a whole column use the button. Once you have selected the contents to change, select one of the modes of change that appear in the upper left corner. The modes of change are:

Insert: Insert the given value at the beginning of the content
Append: Append the given value at the end of the content
Replace: Replace a string in the content with the given value
Clear: Remove the content

After selecting the change mode, enter the text in the field where necessary and click on the corresponding button to perform the changes

Filtering

To filter the content of the table, click in the column that should be used for filtering. Then choose the mode of comparision:

= : The content must be exactly like the given value
~ : The content must contain the given value
≠ : The content must be different to the given value

If you want the filtering to be case sensitive, choose the a<>A option. After all parameters are set, click on the button. To undo the filtering, click on the button. This will reset the data to the last saved version. If you want your changes to be saved, click the button before you reset the filtering. If you close the window all changes so far will be saved automatically. So if you do not want to save your changes, click on the button before closing the window.

Export

To export the data as a tab separated text file, click on the button. The file will be automatically saved in the client-folder.

Log data

To see the log data of the table, you can click on the button. The content of the log table can not be changed, but is read only.

Diversity Scientific terms

Terminology

To edit the terminologies select Administration - Terminologies … from the menu.

A form as shown below will open. A terminology may optionally be linked to a project in DiversityProjects. Click on the button to get further informations about the project or directly access the module DiversityProjects. To remove the connection to DiversityProjects, click on the button.

After changes in the data, especially in the hierarchy, please use the button Refresh the cache entries for the hierarchy to update the hierarchy cache for the terms within the terminology. The hierarchies are build using the preferred terms (see Editing the data ).

On the left the terminologies accessible for the user are listed, on the right you find the details. At the bottom of the window the properties, references and users with access to the selected terminology are listed. In the User tab, use the < and > buttons to decide if a user has access to a terminology. To add missing users use the button. This functionallity is as well available under the Login Administration.

Diversity Scientific terms

Import Export

The import wizard reachable in the menu Data -> Import can be used to import data into DiversityScientifcTerms. Currenlty there is no export wizard, but the data tables from DiversityScientificTerms can be exported using the Table editors, accessible via the menu -> Data -> Table Editors.

Diversity Scientific Terms

Import wizard

The import wizard is the general way to import data into a Diversity Workbench module database. It allows the import from tab separated text files (tsv) into the database tables. The key import steps, the definition of a mapping from tab seperated columns in the text file to the coresponding database table columns, is designed in the import wizard. As the mapping can be sometimes cumbersom to develop, the import wizard allows to save the mapping for repeated import of equaly structured tsv files.

The examples below are from the module DiversityAgents, but are valid for any other module as well.

With the current solution please ensure that there are no concurrent imports in the same database.

With this import routine, you can import data from text files (as tab-separated lists) into the database. A short introduction is provided in a video . Choose Data → Import → Wizard → Agent from the menu. A window as shown below will open that will lead you through the import of the data. The window is separated in 3 areas. On the left side, you see a list of possible data related import steps according to the type of data you choose for the import. On the right side you see the list of currently selected import steps. In the middle part the details of the selected import steps are shown.

Choosing the File and Settings

File: As a first step, choose the File from where the data should be imported. The currently supported format is tab-separated text. Choosing a file will automatically set the default directory for the import files. To avoid setting this directory, deselect the option Adapt default directory in the context menu of the button to open the file.
Encoding: Choose the Encoding of the file, e.g. Unicode. The preferred encoding is UTF8.
Lines: The Start line and End line will automatically be set according to your data. You may change these to restrict the data lines that should be imported. The not imported parts in the file are indicated as shown below with a gray background. If the
First line: The option First line contains the column definition decides if this line will not be imported.
Duplicates: To avoid duplicate imports you can Use the default duplicate check - see a video for an explanation.
Language: If your data contains e.g. date information where notations differ between countries (e.g. 31.4.2013 - 4.31.2013), choose the Language / Country to ensure a correct interpretation of your data.
Line break: With the option Translate \r\n to line break the character sequence \r\n in the data will be translated in a line break in the database.
SQL statements: To save all SQL statements that are generated during a test or import, you can check the option Record all SQL statements.
Schema: Finally you can select a prepared Schema (see chapter Schema below) for the import.

Choosing the data ranges

In the selection list on the left side of the window (see below) all possible import steps for the data are listed according to the type of data you want to import.

The import of certain tables can be paralleled. To add parallels click on the button (see below). To remove parallels, use the button. Only selected ranges will appear in the list of the steps on the right (see below).

To import information of logging columns like who created and changed the data, click on the include logging columns button in the header line. This will include additional substeps for every step containing the logging columns (see below). If you do not import these data, they will be automatically filled by default values like the current time and user.

Attaching data

You can either import your data as new data or Attach them to data in the database. Select the import step Attachment from the list. All tables that are selected and contain columns at which you can attach data are listed (see below). Either choose the first option Import as new data or one of the columns the attachment columns offered like SeriesCode in the table Series in the example below.

If you select a column for attachment, this column will be marked with a blue background (see below and chapter Table data).

Merging data

You can either import your data as new data or Merge them with data in the database. Select the import step Merge from the list. For every table you can choose between Insert, Merge, Update and Attach (see below).

The Insert option will import the data from the file independent of existing data in the database.

The Merge option will compare the data from the file with those in the database according to the Key columns (see below). If no matching data are found in the database, the data from the file will be imported. Otherwise the data will be updated.

The Update option will compare the data from the file with those in the database according to the Key columns. Only matching data found in the database will be updated.

The Attach option will compare the data from the file with those in the database according to the Key columns. The found data will not be changed, but used as a reference data in depending tables.

Empty content will be ignored e.g. for the Merge or Update option. To remove content you have to enter the value NULL. As long as the column will allow emty values, the content will be removed using the NULL value.

Table data

To set the source for the columns in the file, select the step of a table listed underneath the Merge step. All columns available for importing data will be listed in the central part of the window. In the example shown below, the first column is used to attach the new data to data in the database.

A reminder in the header line will show you which actions are still needed to import the data into the table:

Please select at least one column = No column has been selected so far.
Please select at least one decisive column = If data will be imported depends on the content of decisive columns, so at least one must be selected.
Please select the position in the file = The position in the file must be given if the data for a column should be taken from the file.
Please select at least one column for comparison = For all merge types other than insert columns for comparison with data in the database are needed.
From file or For all = For every you have to decide whether the data are taken from the file or a value is entered for all
Please select a value from the list = You have to select a value from the provided list
Please enter a value = You have to enter a value used for all datasets

The handling of the columns in described in the chapter columns.

Testing

- To test if all requirements for the import are met use the Testing step. You can use a certain line in the file for your test and then click on the Test data in line: button. If there are still unmet requirements, these will be listed in a window as shown below.

If finally all requirements are met, the testing function will try to write the data into the database and display any errors that occurred as shown below. All datasets marked with a red background, produced some error.

To see the list of all errors, double click in the error list window in the header line (see below).

If finally no errors are left, your data are ready for import. The colors in the table nodes in the tree indicate the handling of the datasets:

INSERT
MERGE
UPDATE,
No difference
Attach
No data

The colors of the table columns indicate whether a column is decisive , a key column or an attachment column .

If you suspect, that the import file contains data already present in the database, you may test this and extract only the missing lines in a new file. Choose the attachment column (see chapter Attaching data) and click on the button Check for already present data. The data already present in the database will be marked red (see below). Click on the button Save missing data as text file to store the data not present in the database in a new file for the import. The import of agents contains the option Use default duplicate check for AgentName that is selected by default. To ensure the employment of this option the column AgentName must be filled according to the generation of the name by the insert trigger of the table Agent (InheritedNamePrefix + ' ' + Inheritedname + ', ' + GivenName + ' ' + GivenNamePostfix + ', ' + InheritedNamePostfix + ', ' + AgentTitle - for details, see the documentation of the database).

If you happen to get a file with a content as shown below, you may have seleted the wrong encoding or the encoding is incompatible. Please try to save the original file as UTF8 and select this encoding for the import.

Import

- With the last step you can finally start to import the data into the database. If you want to repeat the import with the same settings and data of the same structure, you can save a schema of the current settings (see below). You optionally can include a description of your schema and with the button you can generate a file containing only the description.

Schedule for import of tab-separated text files into DiversityAgents

Target within DiversityAgents: Agent
Database version: 02.01.13
Schedule version: 1
Use default duplicate check: ✔
Lines: 2 - 7
First line contains column definition: ✔
Encoding: UTF8
Language: US

Lines that could not be imported will be marked with a red background while imported lines are marked green (see below).

If you want to save lines that produce errors during the import in a separate file, use the Save failed lines option. The protocol of the import will contain all settings according to the used schema and an overview containing the number of inserted, updated, unchanged and failed lines (see below).

Description

- A description of the schema may be included in the schema itself or with a click on the Import button generated as a separate file. This file will be located in a separate directory Description to avoid confusion with import schemas. An example for a description file is shown below, containing common settings, the treatment of the file columns and interface settings as defined in the schema.

procFillJsonCache is started by an update trigger trgUpd… of the main table in the database

Interface in clients

All modules provide data via a cache table. In the header of the clients you can inspect the content of the JsonCache with a click on the button. For modules with a difference between local and public data, you can inspect the content of the public data with a click of the right mouse button.

Update

Apart of the update via the Trigger (see below) you can update the JsonCache via the update button underneath the button.

To update the JsonCache for the whole database select Administration - JsonCache… from the menu. a window as shown below will open where you can update the JsonCache for single datasets or the whole database.

Summary

graph TD;
    TaxonName[Main table in database] 
    trgUpdTaxonName[trgUpd.. of main table in database]
    TaxonName --> |Update in table| trgUpdTaxonName
    proc[Procedure procFillJsonCache setting the content in table JsonCache]
    trgUpdTaxonName --> proc

graph TD;    
    Mainform[Main form]
    ButtonShow[Button show JsonCache of current dataset]
    Mainform --> ButtonShow
    Left[Show Data]
    ButtonShow --> |Left click| Left

graph TD;    
    Mainform[Main form]
    Admin[Administration menu]
    Mainform --> Admin
    Cache[JsonCache...]
    Admin --> Cache
    Adminform[Administration form]
    Cache --> Adminform
    AdminUpdateSingle[Update single dataset]
    Adminform --> AdminUpdateSingle
    AdminUpdateDB[Update for whole database] 
    Adminform --> AdminUpdateDB

Diversity Scientific terms

Settings

The settings for the software are stored in a directory created by the application, e.g. C:\Users\[LoginName]\AppData\Local\DiversityWorkbench\[DiversityWorkbenchModule].exe_Url_0he1anjeninqrrxpdywiwnwxaqvlezn3\4.4.13.0 where [LoginName] is the name of the user and [DiversityWorkbenchModule] the name of the Diversity Workbench module e.g. DiversityCollection. This directory contains the file user.config where all settings are stored in xml format. An example for the content in the module DiversityCollection is shown below:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
    <configSections>
        <sectionGroup name="userSettings">
            <section name="DiversityWorkbench.WorkbenchSettings" type="System.Configuration.ClientSettingsSection, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
        </sectionGroup>
    </configSections>
    <userSettings>
        <DiversityWorkbench.WorkbenchSettings>
            <setting name="ModuleName" serializeAs="String">
                <value>DiversityCollection</value>
            </setting>
            <setting name="GenerateTraceFile" serializeAs="String">
                <value>False</value>
            </setting>
            <setting name="DatabaseServer" serializeAs="String">
                <value>zsm.diversityworkbench.de</value>
            </setting>
            <setting name="IsTrustedConnection" serializeAs="String">
                <value>True</value>
            </setting>
            <setting name="DatabaseName" serializeAs="String">
                <value>DiversityCollection</value>
            </setting>
            <setting name="QueryMaxResults" serializeAs="String">
                <value>100</value>
            </setting>
            <setting name="DatabasePort" serializeAs="String">
                <value>5432</value>
            </setting>
            <setting name="DatabaseUser" serializeAs="String">
                <value>User</value>
            </setting>
            <setting name="ResourcesDirectory" serializeAs="String">
                <value>Home</value>
            </setting>
            <setting name="HowToCopyAppToUserDirectory" serializeAs="String">
                <value>Missing</value>
            </setting>
        </DiversityWorkbench.WorkbenchSettings>
        <DiversityCollection.Forms.FormCollectionSpecimenSettings>
            <setting name="SplitContainerData_SplitterDistance" serializeAs="String">
                <value>270</value>
            </setting>
            <setting name="QueryConditionVisibility" serializeAs="String">
                <value>10000100011000010000000000001000000001100000000000000000000000000001110000110110000000000000000000000000000000000000000000000000000000000000000000000000011100001000000000000000010000000000000000001000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000</value>
            </setting>
            <setting name="ImageDisplay" serializeAs="String">
                <value>Hidden</value>
            </setting>
            <setting name="AskOnExit" serializeAs="String">
                <value>True</value>
            </setting>
        </DiversityCollection.Forms.FormCollectionSpecimenSettings>
    </userSettings>
</configuration>

Diversity Scientific Terms

Scope of DiversityScientificTerms within the Diversity Workbench

Subsections of Scientific terms

Diversity Scientific terms

Download

Upcoming version

4.2.1

Current version

4.2 (2023-05-10)

Previous versions

4.1.21 (2023-02-22)

Database updates

Subsections of Download

Diversity Scientific terms

Installation

Resources

Download

Installation of the client

Run program without installer

Technical notes and additional information

Windows protection warning

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Database login

Connect to a database

Previous connection

Testing a connection

Switch between databases

Reset and Cancel

Encryption

Videos

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Menu

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Query

Perform a Query

Display the Entire Dataset

Filter a Search

Edit and Customise Query Conditions

Customise the Interface

Edit the Result List

Add Results to the Existing List

Remove Result Items from the List

Many Result Columns

Query Conditions

Remember the Last Query

Query Annotation

Duplicates

Query Modules

Query any fields

Videos

Wildcards in SQL

Many colunns

Diversity Scientific terms

Editing the data

Display settings for charts etc.

Copy data

Subsections of Editing

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Chart

Ranking terms resp. types

Sections

Images

Colors

Files

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Dependency

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Hierarchy

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History

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Language

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Properties

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Ranking terms

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References

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Resources