Data Editing

Editing the data

The database of DiversityDescriptions consists of three major areas:  

  • The descriptive data (descriptions) reference elements of the descriptive terminology and add specific data, e.g. numeric values.
  • The descriptive terminology, consisting of descriptors, categorical states, statistical measures and modifiers. 
  • The project data build the administrative frame for terminology and descriptions. Each description belongs to exactly one project. By additional entities (descriptor tress) it is possible to restrict the descriptors, statistical measures and modifier that shall be used in a certain project.  

In almost all forms an Extended text editor can be opened for single text fields that provides additional editing features.  

Corresponding with that three major sections of the data model, the DiversityDewscriptions application provide three edit modes. The edit mode is diplayed at the bottom of the main window (see picture below). After the first start the edit mode is preselected to “Edit descriptions”. You can switch the edit mode using the menu Edit-> DescriptionsEdit→ Descriptors or Edit-> Projects. Alternatively you may switch the edit mode by click the mode button in the upper left corner of the header area (item 3 in picture below) or on the tiny triangle besides the edit mode display in the status line at the bottom (see item 4 in picture below).

The main window of the DiversityDescriptions client contains two main areas. At the left you find the query and the results of this query. In the right part the data of the dataset selected in the result list is shown.

 

Basic operations

In each edit mode there are some common functions for storing and reloading data, to create a new dataset or delete or copy the actual dataset. On top of the query results (item 1 in image above) there is button to store the actual dataset, button to delete the actual dataset and button to create a new dataset. By pressing button  the actual dataset is reloaded, i.e. changes that have been made will be dropped. Finally, button copies the data of the actual dataset to a new one.

Some of those buttons can be found in the tool bar at the right side of the edit window (item 2), too.

Additionally to explicit saving by pressing the button, an automatic saving of the dataset is done, if an entry in the query result list is selected or a new query is performed. If a dataset has been modified without saving, a message window will appear and ask if changes shall be saved for several actions, e.g. change of edit mode, connetion to a database or if the application is closed. 

 

Translations

For many database tables the text columns may be translated into different languages. To enter, modify or view the translated texts, use the translations editor. For an overview on multilingualism in Diversity Descriptions see chapter translations.  

 

Description HTML form

When you have started a query and selected a description, you may open an HTML form to view and edit the data (button marked as item 5 in image above). It provides a simplified user interface for access to a subset of the description data. 

 

Description grid view

An alternate form for editing or viewing the data of several descriptions in a grid is provided by the description gridview. It provides a simplified user interface for access to a subset of the description data. 

 

Sample data grid view

An alternate form for editing or viewing the sample data of several descriptions in a grid is provided by the sample data gridview

 

Table editors

For a selected set of database tables a direct data editing in a grid is provided by the table editors

 

Jan 14, 2025

Subsections of Editing

Edit Description

Editing the description

After starting a database query and selecting an entry in the result list the dataset is diplayed in the edit window. In the header area the dataset name, the default project language and the URI of the current dataset are show (see picture below). Below the header area the description name may be edited in a text box. Changes of the description data, e.g. the name, will be visible in the header after saving the dataset. To check dataset changes, click on the button to open the history. By clicking button you may open a simplified HTML form to view and edit the description data.

The main description data may be accessed in the first Mainattributes tab, which is described below. Click on one of the other tabs in the picture below to go directly to the appropriate manual chapter.

img/DD_Description_Main

 

Main attributes tab

The main attributes tab provides in the upper area a field to enter additional description details and a wording for natural language support. The optional filed AID may keep an alpha-numeric alternate ID of the dataset. If used, it should be unambigious within the project, but this is not checked by the program. Click on to get an overview of the used keys. 

 

Scopes

The next section Description scopes allows specification of description scopes. This sections consists of the scope table with scope type and value and a edit section to modify a seleted scope entry or to enter e new scope. The scope types Geographic ares, Reference, Specimen, Observation and Taxon name allow input of a free-form text or reference to the corresponding DiversityWorkbench module or a web service. The connection to to a module or web service is done using the button . After selecting the entry in the referenced database the text will be taken over and the backround colour of the scope value field changes to yellow. A further editing of the text will not be possible (see below).

 

Additionally the edit section now shows the buttons to view the database link and  to remove the database link. In the latter case editing of the scope value will be possible again.

If a scope entry has been selected in the scope table, it can be modified in the edit section. If you want to enter a new scope value instead, press the button at the end of the edit line. The scope entry in the scope table will be deselected and a selection box for the scope type appears in the edit section (see below).

You may insert mutiple scope values with links to a DiversityWorkbench module or a webservice. Therfore enter a new scope value with scope type Geographic ares, Reference, Specimen, Observation and Taxon name (or select one, which is not yet linked). Besides the scope type dropdown box the button is shown, which allows insert of multiple scopes (see image below).

You may insert mutiple scope values with links to a DiversityWorkbench module or a webservice. Therfore enter a new scope value with scope type Geographic ares, Reference, Specimen, Observation and Taxon name (or select one, which is not yet linked). Besides the scope type dropdown box the button is shown, which allows insert of multiple scopes (see image below).

In the remote query panel you find the section Unit list, where you may add the currently selected query result by clicking the button. When you select an entry in the Unit list, you may remove it by clicking or view the data in a separate window by clicking . When you have collected all query results click the OK button and the scopes are inserted for the description (see below).

 

Project scopes

Besides the already mentioned scope types that allow input of a free text or reference to a database entry, the scope types Sex, Stage, Part and Other scope provide pre-defined scope values. The values can be administrated as described in the Editing theProject chapter. For each project a different set of values can be selected as “recommended” values. If for the current description project scope values are defined/assigned, they are shown in the right part of the description scopes as Project scopes (see below).

Selecting or deleting of a scope entry can be easily done by selecting clickin on the check box before the scope value. You may select rsp. deselect all scope values of a certain scope type (Sex, State, Part or Other scope) by clicking the check box of the category. If for a scope value a detailled description text has been stored, you may view it as bubble help by moving the mous cursor over the values.

If for a description a scope value is selected, that is not assigned to its project, the value ist show with yellow background (see below). Such a situation can occur, if the scope value has been removed for the project or if a description has been moved to a different project. 

 

Project

The section Project allows the selection of the project the description is assigned to. This adjustment has influence of the available values of scope types Sex, Stage and Other scope, the available descriptors and recommended modifier/frequency values and statistical measures of the description. Therefore this unambiguous adjustment might be seen as the “terminology project” of the description item. The access rights for a certain user to the projects are controlled with the login settings (see chapter Loginadministration). When you click on a project name, you may view some additional project data (see image below middle). 

     

If access to a certain project is restricted to “read only”, it is displayed with grey colour and symbol in the Project section (see pictures above). A “read only” project cannot be selected for the actual description. If the selected description has already been assigned to a “read only” project by another user with appropriate rights, this is indicated at the right bottom corner of the application window (see above below right).

 

Additional projects

In section Additional projects you may make the description accessible for additional projects. To assign a description to a project click on the  button. To remove it from a project, select the project from the list and click on the  button. Additional projects without write access are shown in the upper part of the window, projects with full access in the lower (or only) part (see image below). If you do not have any access to a project, it is shown as red text. Be aware that by entering additional projects you may grant editing rights for single descriptions to users that have no write access to the current project!

     

Be aware that by entering additional projects you may grant editing rights for dedicated descriptions to users that have no write access to the current project! If you have write access to the terminologyproject of a description item and granted access to another project, where you have read-only access, you nevertheless may withdraw these rights by removing it from the Additional projects.

   

 

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Jan 14, 2025

Subsections of Edit Description

Edit Description Continuous View

Editing the description - Continuous view tab

The continuous view tab provides an alternate view on the descriptive data. In the Summary data only the descriptors are included where data have been entered. At the right side there is a tool strip. The displayed buttons will change depending on the selected entry. The descriptor types categorical, quantitive, text and sequence are indicated by different colours and icons as shown in the example at the bottom. By pressing the button on the tool strip this example may be hidden. Descriptors that are marked as mandatory are displayed with light red text, descriptors that are inapplicable are greyed out. Additionally coloured background indicated possible problems, e.g. if an inapplicability rule has been ignored or a not allowed descriptor has been used. A tool tip text shows the error or warning reason when the mouse curser is moved over the element.

By pressing the button the tree view may be expanded to display the contained categorical states, quantitative measures or texts. By pressing the button the tree will be collapsed to descriptor level.

To insert a descriptor press , to delete a descriptor select the entry and press . If only a single value shall be removed, select the entry and use the button. All these functions can alternatively be accessed by the context menu by a right-click on the tree node.

If for a descriptor resources, e.g. pictures, are avaialble, this is indicated by the background color of the descriptor icon. Categorical states with resources are marked with icon (see first entries in picture above). The resources may be accessed by a right-click on the tree node and selecting context menu item View resources (see picture above).

 

Structured descriptor view

If for the project a structured descriptor tree is defined, i.e. a descriptor tree that contains at least one descriptor tree node, the Descriptor tree: drop-down list is shown below the descriptor tree (see image below left). If a descriptor tree is selected, the descriptor tree node hierarchy will be included in the output and the descriptors will be arranged accordingly. The names of the descriptor tree nodes and the descriptors will be reduced by parts contained in the supriour hierarchy nodes (see image below right).  

If for a descriptor tree node resources are available, this is indicated by the grey background color of the descriptor tree icon. The resources may be accessed by a right-click on the tree node and selecting context menu item View resources. Additional descriptor tree node information, e.g. an optional abbreviation or details text can be viewed as bubble help by placing the mouse cursor over the item.  

 

Editing summary data

A click on opens an edit window at the right part of the tab. This window provides the same functions as available in the descriptor view tab. The picture below shows the resource linked to a categorical state that can be opened by doule-clicking the state ID in the Categorical states section. 

 

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Jan 14, 2025

Edit Description Descriptor View

Editing the description - Descriptor view tab

The left part of the descriptor view tab shows all descriptors available for the description’s project. The entries in column “!” indicate some additional information about the descriptor:

  • Descriptor is referenced in the summary data (●)
  • Descriptor is referenced in the status data (○)
  • Descriptor is mandatory, values must be specified (!)
  • Descriptor is inapplicable because of other specified descriptors/categorical states (x)
  • Descriptor is exclusive, only one categorical states shall be selected (e)

If resources are linked to a descriptor, the entry is marked by a square (□) behind its sequency number and a tool tip appears when the mouse cursor is moved over the “No.” column (see below). By double-clicking the sequence number a “Media view” window can be opened to view the resources.

 

If for the project descriptor trees are defined, the Descriptor tree: drop-down list and Restricted check box are shown below the descriptor list (see image below left). If a descriptor tree is selected, the names of the descriptor tree node hierarchy is included in the descriptor names (see image below right). This feature is useful, if several descriptors with ambigious names exist the can now be distinguished. E.g. two descriptors “colour”, one at descriptor tree node “Leaf”, the other at descriptor tree node “Blossom” will become “Leaf colour” and “Blossom colour”. If the descriptor name already includes the hierarchy, the duplicate parts will be filtered. In the mentioned example the descriptor names “Leaf colour” and “Blossom colour” will not be changed, if the descriptor tree is selected.

If additionally the Restricted option is set, only the descriptors included in the selected descriptor tree are displayed (see image below right, missing descriptor number 14). So you have the option to create several descriptor trees that include only special aspects of the description’s property (e.g. morphology, molecular biology and so on) to get a clearly arranged descriptor list. 

 

Editing summary data

The right part of the descriptor view tab shows at the bottom the Status data values of the selected descriptor. It is possible to select several values for each descriptor. In the “Notes” column additional information concerning the selected data status may be entered. By a double click on the “Notes” entry a separate edit window can be opened.

Depending on the descriptor type you can find at the top either Categorical states (see large picture above), Statistical measures, Descriptive text or Molecular sequence (see pictures below). In the “Notes” columns additional information concerning the specific categorical state rsp. statistical measure may be entered. By a double click on the “Notes” entry a separate edit window can be opened.

  

To enter a statistical measure value click in the “Value” field and enter the value, the check mark in field “x” will be set automatically. If recommended modifier values are defined (see “Editing the Descriptor” and “Editing the Project”), a value may be selected from the drop down list “Modifier”. If no modifier values are available, the appropriate table column may be hidden. In the “Notes” field an additional text may be added. By double-clicking the “Notes” field the Extended texteditor can be opened.

The descriptive text may be edited diretly in the window, which shows the pure text without any formatting. In the notes field an additional text may be entered. By double-clicking the text fields the Extended text editor can be opened. 

The molecular sequence window displays in the status line below the edit area the sequence type (“Nucleotide” or “Protein”), the symbol length (“Len:”) in case of proteine sequences, the gap symbol (“Gap:”) if defined, the long text of the actual element and the position (“Pos:”) (see image below). In case of three-letter proteine symbols the position is the number of the amino acid symbol, not the character position. By pressing the TAB key the cursor jumps to the next symbol. 

When characters are entered in the edit area that are recognized as valid symbols, they will automatically be formatted. One-letter symbols are converted to upper case characters, three-letter symbols are converted according the “Xxx” schema, e.g. “Ala” for “Alanine”. The sybols for the nucleotide bases "Adenine", "Cytosine", “Guanine”, "Thymine" and "Uracil" are dispayed with different colors. Ambiguity symbols and gap symbols are shown in grey color. If the ambiguity symbols have not been enabled in the descriptor data, they will be displayed with yellow background. Symbols that have not been recognized are displayed with red background. 

The molecular sequence window offers some additional functions available in the sequence menu. It may be opened by moving the mouse cursor over the control header (“Molecular sequence”, see window below left) or from the context menu (right-click on the sequence edit area, see windows below right). With menu item Import you may read the seqeunce data from a file and insert them to the description. With menu item Export you may export the actual sequence data to a file.  

   

By double-clicking the molecular sequence area or from sequence menu Open → Sequence a separate edit window may be opened (see image below). On the top of the window there is the drop-down menu Insert symbol: where a value may be selected from a list. After selecting the value press the [ENTER] key or click on to insert the selected symbol at the cursor position. 

To select a categorical state set a check mark in field “x” with a mouse click. If recommended modifier or frequency values are defined (see Editing the Descriptor and Editing the Project), values may be selected from the drop down lists “Modifier” rsp. “Frequency”. If no modifier or frequency values are available, the appropriate table column may be hidden. In the “Notes” field an additional text may be added. By double-clicking the “Notes” field the Extended text editor can be opened. 

If a “Modifier” or “Frequency” value is selected, the multiple specification of a dedicated categorical state is possible. A tool tip offers to add a row by doouble-click, if mouse cursor is moved over the “State” field (left picture below, picture in the midddle after double click). Multiple specifications of one categorical state are only allowed if they have been assigned different modifier and frequency values. Inputs offending these restrictions will be ignored an a cell error will indicate the problem (right picture below).

   

If resources are linked to a categorical state a tool tip appears when the mouse cursor is moved over the ID (left picture below). By double-clicking the ID a “Media view” window can be opened to view the resources (right picture below).

 

If more than one resources have been assigned to one entry, a slider will be visible at the bottom of the “Media view” window. To switch through the available resources the slider can be moved using the mouse or the right and left arrow keys (see below).

 

 

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Jan 14, 2025

Edit Description HTML

Edit description in HTML form

With this form you can easily edit the description data in an HTML form. After starting a description query and selecting an entry choose Edit -> Edit as HTML form … from the menu or click on the button at the right side of the main Diversity Descriptions window. A window as shown below will be opened.

 

When you move the mouse cursor over embedded pictures, they are slightly magnified, by clicking on the resource, you may show it in full size (see below). Use button  Home to return to the HTML form. 

 

With drop down button Options you may insert some additional input fields in the form, e.g. item details or notes. With drop down button Scope you may insert input fields for the vasiour scope types and drop down button Color lets you select the background color. All that changes come into affect, when you reopen the form or redraw the HTML form using the Reload button.

After clicking the Reload button you will be asked if you want to discard all changes. By selecting No the HTML form data will be written into the local data store, otherwise all inputs will be reset. To exit the form and save all changes in the local data store, click the OK button. To ignore your changes, click the Cancel button and you will be asked if you want to discard all changes. The HTML form utility works completely on the local data store. I.e. if you edited the description data in the main form of Diversity Descriptions and start the HTLM form editor without saving the data, all changes are only present in the application dataset. To store the data in the database, click the save button of the main form!

 

 

May 3, 2024

Edit Description Molecular Sequences

Editing the description - Molecular sequence symbols

The editor for sequence data recognizes predefined symbols for nucleotide and protein sequences according the IUPAC definitions.

 

Nucleic acid symbols

Symbol Name
A Adenine
C Cytosine
G Guanine
T Thymine
U Uracile
W Weak (A or T) 
S Strong (G or C)
M aMino (A or C)
K Keto (G or T)
R puRine (G or A)
Y pYrimidine (C or T) 
B not A (B comes after A) 
D not C (D comes after C)
H not G (H comes after G)
V not T (V comes after T and U)
N No idea (not a gap)

The symbols with grey background are ambiguity symbols. The difference between “N” and a gap symbol (usually “-”, but any other symbol may be defined in the descriptor) is that a gap symbol represents an unspecified number of unknown symbols but “N” stands for exatly one nucleic acid. 

 

Amino acid symbols

Name 1-letter sybmol 3-letter sybmol
Alanine A Ala
Arginine R Arg
Asparagine N Asn
Aspartic acid S Asp
Cysteine C Cys
Glutamic acid E Glu
Glutamine Q Gln
Glycine G Gly
Histidine H His
Isoleucine I Ile
Leucine Leu
Lysine K Lys
Methionine M Met
Phenylalanine F Phe
Proline P Pro
Serine S Ser
Threonine T Thr
Tryptophan W Trp
Tyrosine Y Tyr
Valine V Val
Selenocysteine U Sec
Pyrrolysine O Pyl
Asparagine or aspartic acid B Asx
Glutamine or glutamic acid Z Glx
Leucine or Isoleucine J Xle
Unspecified or unknown amino acid X Xaa

The symbols with grey background are ambiguity symbols. The difference between “X” rsp. “Xaa” and a gap symbol (e.g. “—”, but any other symbol may be defined in the descriptor) is that a gap symbol represents an unspecified number of unknown symbols but “X” rsp. “Xaa” stand for exatly one amino acid. The amino acids “Selenocysteine” and Pyrrolysine" are non-standard amino acids that only occur in certain species. 

 

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Jan 14, 2025

Edit Description Resources

The resouce links tab allows assigment and inspection of resource links for the description. In the lower Resources part of the tab there are two tables. Ar the left the “Resource” table specifies the single resources, at the right the “Resource variant” table contains the associated URLs to images, video or sound resources.

To enter a new resource select the empty line at the end of the “Resource” table and click on the “Resource name” field. After entering the “Resource name” (leave the cell by pressing the TAB key) automatically a new value for the sequence number (“No.”) is initialized. The sequence number determines the display order in tables and may be changed manually. You may order the resource entries by clicking on the column header or by using the arrow buttons in the left tool strip ( and for up and down, and to shift the selected entry to top or bottom). After ordering the resources click button to renumber the entries starting with “1” and make the changes effective. In field “Ranking” you may enter a numeric value in range 0 … 10 expressing the suitability of the resource. In field “Role” you may select one of the offered values.

If you want to delete a resource, you have three choices:

  1. Select the resource and press the button in the left tool strip.
  2. Select the resource and press the Delete key on the keyboard.
  3. Enter the sequence number column (“No.”) and remove the value. After leaving the cell the entry will be deleted.

In any case you will be asked if you want to delete the data row, if resource links are present. 

To view or edit the additional resource data and copyright information press on the button besides the resource table. In field License: and a link to the license text in the web may be entered, in field Rights: you may enter a copyright text. By pressing the button a browser window can be opened to navigate to the license page in the web. Furthermore you may enter a detailled text (field Details:), the resource language (field Language:) and set the Display embedded flag (see picture below). If any additional resource data have been entered, this will be indicated by a square (□) behind the resource name’s sequence number (see picture above).

 

To enter a resource link, first select the entry in the “Resource” table, then select the empty line at the end of the “Resource variant table”. By clicking on the “URL” field a web address may be entered. By double-clicking the “URL” field a browser window opens to navigate to the resource. For each resource several URLs to resource variants with different quality levels, e.g. different resolution, may be inserted. For each entry in the URL table a different value of “Variant” must be selected.

As an alternative to a resource URL a colour may be spcified in the format “color://#rrggbb” where “rrggbb” specifies a hexadecimal colour code. The colour can simply be seleced by clicking the button besides the resource variant table.

To remove a resource variant, select the entry and press the button in the right tool strip or the Delete key on the keyboard. Alternatively you may delete the “URL” entry in the resource variant table. 

The button besides the resource variant table allows you to view a resource URL in the system browser.

The upper part of the resource links tab consists of a preview window on the left side and the complete list of resource links. By selecting one of the links the preview is shown on the preview window. If you press button in the preview window, the resource is opened in a separate viewer window.

At the bottom of the resource links tab the media data of a selected URL are displayed. These data can be edited by double-clicking the “Type” entry in the resource variant table, by clicking at one of the media data value fields or the button. The edit dialog provides the possibility to access the URL to get available data. Additionally the values may be edited manually.   

 

Copy description resources to a descriptor

If you have write access to descriptors of the currently selected description’s project, you may copy a selected resource URL to a descriptor. After clicking the button a window will open to select one of the accessible descriptors (see image below). Remark: To see the copied resources in the Descriptorview or the Continuous view, you will have to reconnect to the database. 

 

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Jan 14, 2025

Edit Description Samples

Editing the description - Sample data tab

The sample data tab allows assigment and inspection of sampling events and associated sampling units for the description. In the upper left Sampling events part of the tab there is a list of the sampling events stored for the description. By selecting a sampling event entry the Event data are shown in the upper right part of the tab. Here you may edit the event name, a detailled description, the date and time rsp. a date and time span and geographic data. To insert a new sampling event click on the button in the Sampling events section, to delete the selected sampling event and all stored sampling unit data press the button (see image above). 

The geographic area may be linked to an entry of a DiversityGazetteers database (see section Module related entry). If latitiude and longituede have not yet been entered, the coordinates of the selected DiversityGazetteers entry will be inserted. By pressing the button a window to select the coordinates by Google maps will be opened. Field Geo. datum allows entering short text concerning the geodetic datum. If coordinates are entered using Google maps a remark that WGS84 coordinates are used will be inserted.

 

Editing sampling unit data

For each sampling events one or several Sampling units may be entered. A sampling unit represents a tuple of values that belong together, e.g. because they represent a single specimen. For each descriptor, which is represented by the table column, a value may be entered in a sampling unit, which builds a single table line. The background colour of each table column indicates the type of sample data: categorical, quantitative, text or sequence . If the number of sampling units is displayed in field Units of the Sampling units section in the lower part of the tab. If sampling units are present, the number is displayed with yellow background (see image below).

To view the unit data, select a Descriptor tree and choose the descriptor sequence range (From descriptorto descriptor) to restrict the number of columns displayed in the unit table. Finally press button and the sampling untis will be displayed (see image below). If you prefer to display the present sampling units automatically whenever you select a sampling event, click on the number behind Units. The background changes from yellow to red to indicate this mode. When you select a cell and resources are available for the selected descriptor column, the button will be shown. You may click it to view the descriptor resources. 

To insert a new sampling unit press button . By clicking on the free space at the beginning of a table line you mark the whole sampling unit (see picture below). Now you have the additional options to delete the unit by pressing button or to copy the data to a new sampling unit by pressing the button. Keep in mind that all unit data will be copied, even if you do not see all descriptor columns due to the display restrictions.

 

When you select the Sampling unit ID cell you may enter a collection specimen in the Unit specimen control below the units table. By clicking the button (see section Module related entry) you can link it to an entry in a DiversityCollection database. If the sampling unit is linked to a database entry in DiversityCollection, the text of the Unit specimen: control is shown with light yellow background. You may view the linked data by clicking the button or double clicking the Sampling unit ID cell.

To modify categorical sampling data enter the table cell and press the button within the cell. A control will be opened where you can select the categorical states and enter notes or modifier values (if defined) for each single state (see image below).

 

For all other sampling data the value can be entered directly in the table cell. Notes for the selected table cell are entered in the Notes: text box directly below the units table. For categorical, text and molecular sequence sample data a separate edit window can be opened by double-clicking the table cell. For molecular sequence data the tool strip buttons (import) and  (export) allow import and export from rsp. to dedicated file formats as described in sections Import sequencedata and Export sequence data.

 

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Jan 14, 2025

Export Sequence

Editing the description - Export sequence data

With this form you can export data from the database to a file. Choose Export from the sequence menu to open the window for the export. Format specifies the file format, currently FASTA and FASTQ are supported.

 

In the Header settings you may specify if a new header shall be generated or if the notes shall be searched for a FASTA rsp. FASTQ header. In case of FASTA export you may specify in the Comments settings section if FASTA comment lines from the notes (starting with “;”) shall be inserted after the header, the whole notes shall be inserted as FASTA comments or if the notes shall be ignored. If Insert description comments is checked, two comment linsed wit the description and descriptor title will be generated.

In the Header preview section you may check and edit the resulting header, in the Sequence preview section the converted sequence in one-letter notation is displayed.

In case of FASTQ export the Comments settings are irrelevant. If the notes include a QUALITY STRING sections, it is inserted in the FASTQ output (see image below). If no quality string can be found or the Find FASTQ quality from notes has been unchecked, the lowest quaality value “!” is inserted.

 

Click on the button to select the file where the data shall be exported. By default the data are appended at the end of the selected file, check the Overwrite existing file option to overwrite it. Finally click the Save file button to write the data.

 

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Jan 14, 2025

Edit Description Grid

Description grid view

After starting a database query for descriptions select Grid → Description grid view … from the menu. The query result list is passed to the description grid view form and a window as shown below opens (click the button Display description table to build the table output). In the first line the database name is displayed. If you move the mouse cursor over the database name, a tooltip shows the actual connection paramter. 

img/DD_Description_Main

The table in the lower part of the window shows the description titles in the first column and the summary data in the other columns. Each summary column holds the data of a certain descriptor. If a cell with summary data is selected, the summary details and the descriptor status data are displayed in the upper right part of the window. The upper left part of the window shows the selection parameters that are used for building the description table. You may change the table colors by clicking the button . A form as shown below will be opened. 

Click on buttons categorical, quanitative, text or sequence to select the corresponding table colors. By clicking the Reset button below the color, the corresponding default value will be selected. After changing the table colors by a click on the OK button, you must re-draw the table.

 

Selection parameters

In the upper left part of the parameters for the description table can be adjusted. If in the query list passed to the form descriptions of different projects are present, the displayed project can be selected with the Project: drop-down box. The entries in the drow-down list include the project name, followed by the number of descriptions for that project in brackets and an asterisk (*) if the user has only read access for that project.

The Descriptor tree drop-down box restricts the descriptor columns to the descriptors contained in the selected tree. Furthermore the tree hierarchy is included in the descriptor names if a structured descriptor tree is selected (see images below).

  

The values From descriptor and to descriptor limit the range of descriptor sequence numbers that is included in the discription tabe. Be aware that this restiction is additionally effective to a selected desriptor tree! If you want to de-activate this restriction, select “from” value 0 “to” value 999999 by a double-click on the labels From descriptor rsp. to descriptor. The limitation of the number of descriptor columns makes speeds up the description table generation, especally if many descriptor (e.g. some hundrets) are present.

If you select option Separate statistical measures, separate columns will be insterted in the data grid for each quantitative descriptor and its recommended statistical measures. This option may be useful for editing quantitative summary data that use other statistical measures than Min, UMethLower, Mean, UMethUpper and Max (see section Data editing for details.

Finally click the button Display description table to build a new description table according to your settings. During output of the description table the icon of the button changes to  and you may abort processing by clicking the button. 

 

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Jan 14, 2025

Subsections of Edit Description Grid

Edit Description Grid Copy

Description grid view - Copy or create descriptions

To copy one or more descriptions select the whole data rows by clicking in the area left from the “Description title” column. In the tool strip the copy button appears (see image below).

img/DD_Description_Main

After clicking the button you may be asked if you want to copy description resources, too. Be aware that the copy operation is directly performed within the database. I.e. that local changes that have been done in the sources desrcriptions will not be included in the targets unless you save your data before copy (see image below, second and last line in descriptors 28 and 29). 

img/DD_Description_Main

 

New description

To enter a new description, click on button and a new row will be appended (see image below). Same as for copy the new description is created directly within the database.

  

 

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Jan 14, 2025

Edit Description Grid Editing

Description grid view - Data editing

The first column of the description table shows the description titles, which are fixed. I.e. if you scroll the summary data to the right, the titles are still visible at the left. The other columns show the summary data, where the descriptor type is indicated by the background colour: categorical, quantitative, text or sequence. The column titles include the descriptor name, the mesurement unit in square bracket for quantitative descriptors and the descriptor’s sequence number (see image below).

When a summary cell in the description table is selected, the field Description: shows the description title and field Descriptor: shows the symbols according the descriptor type ( for categorical, for quantitative, for text and for sequence) and the descriptor title. If for a descriptor resources are available, this fact is indicated by a coloured symbol background. You may view them by a double-click on the descriptor title. If for a description resources are available, the symbol is displayed before the title. Double click in that symbol to view the resources. 

For the selected cell the summary data and the descriptor status data are displayed in the upper right area of the window (see image above). You may edit the data within these controls as described in section Editing the description - Descriptor view tab of this manual. For modified summary cells the text colour changes to blue and the description titles will be shown with yellow background in the table.

 

Changing the description title

To change the description title, double-click on it in field Description: to open a separate edit window. After comitting the changes with “OK” the description will be marked as modified (see images below).

  

 

Changing the summary data in the table

Categorical summary data

Categorical, states are specified by their sequence number. Multiples are separated by a forward slash ("/", see image below). Existing “notes” will be removed, if the corresponding categorical state is not specified in the input.

  

 

Quantitative summary data

If you did not check the option Separate quantitative measures, for quantitative summary data only the five quantitative measures  

Min Minimum value
UMethLower Lower range limit (legacy data stat. meth. unknown)
Mean Mean (= average)
UMethUpper Upper range limit (legacy data stat. meth. unknown)
Max Maximum value

can be specified within the summary table. The values must be specified in theis given order and separated by a forward slash ("/"). E.g. 1////100 means “Min=1, Max = 100”. If only one value without any slashes is entered, it is assumed than only the “Mean” value is specified. To indicate that values for other than the five mentioned statistical measures are present in the data, an asterisk ("*") is appended in the summary table (see image below, cell value 1////100 *).

  

 

If you checked the option Separate quantitative measures, for each statistical measure in the quantitative summary data a separate column will be allocated in the data grid view. I.e. you can direcly enter your values into the table (see image below).

  

 

Text descriptor and Molecular sequence data

For Text and sequence data the texts may be edited directly within the table. The corresponding “notes” will not be affected.

 

Changing values in a table column

It is possible to modify several values of a single table column. Therefore select the table entries that shall be edited - by selecting an entry and clicking the button in section Column action you may select the whole table column (see image below). Then select the required operation: “Insert”, “Append”, “Replace” or “Clear” and enter the new rsp. new and old value. After clicking the action button - depending on the selected Column action this is (Insert), (Append), (Replace) or (Clear). Be aware that this feature performs a pure text operation in the table columns. Especially for quantitative and categorical data columns the resulting data will be interpreted according to the rules described above an might lead to unsexpected results, if not designed ver carefully. 

 

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Jan 14, 2025

Edit Description Grid Save

Description grid view - Save or discard changes

When you click in button “OK” the description grid view is closed and all changes are automatically saved in the database. If you did some changes and want to save them without leaving the form, simply click on (see image below). If you close the window, e.g. by clicking the “Cancel” button, and still have unsaved changes, you will be asked to save or discard the changes.

img/DD_Description_Main

 

Undo all changes

You may discard all unsaved changes without leaving the form by clicking the button and the data will be reloaded form the database (see image below).

  

 

May 3, 2024

Edit Descriptor

Editing the descriptor

After starting a database query and selecting an entry in the result list the dataset is diplayed in the edit window. In the header area the dataset name is shown (see picture below). Below the header area the descriptor name may be edited in a text box and the sequence number (No.) can be set, which determines the display order in descriptor lists. Changes of the descriptor name will be visible in the header after saving the dataset. To check dataset changes, click on the button to open the history.

The main descriptor data may be accessed in the first Main attributestab, which is described below. Click on one of the other tabs in the picture below to go directly to the appropriate manual chapter.

img/DD_Descriptor_Main

 

Main attributes tab

The main attributes tab provides access to an abbreviation, a detailled descriptor text, notes and wording information for natural laguage descriptions. In the bottom area the Descriptor type, Descriptor settings, Measurement data (only for quantitative descriptors) and Molecular sequence data (only for sequence descriptors) can be adjusted. The descriptor type can only be modified, if the descriptor is not referenced by any description. If the descriptor type “Categorical” is changed, already entered categoricalstates will be deleted.

The check box Exclusive (only for categorical descriptors) indicates that only one state shall be specified in a description. Check box Mandatory indicates that for this descriptor always data shall be specified. Statistical measurement scale specifies for categorical descriptors, if the states are unordered (e.g. red/green/blue) of ordered (e.g. bad/medium/good). For quantitative descriptors it specifies if intervals or ratios are measured. Repeatability and Availability specify how reliable (different measurements or scorings by different observers) and accessible the descriptor is, e.g. for identification.

For quantitative descriptors the Unit of the measurement values my be specified either by directly entering the string or alternatively by selecting a Prefix (e.g. “k” for “kilo” = 1000) and the Base unit (e.g. “g” for “gramm”). Unit is prefix indicates that the measurement unit preceeds the measurement value. Minimum and Maximum specify the absolute range limits expected for the measurement values. If in a description specific values, e.g. “Mean”, exceed these limits, a warning will be shown. Values are integer indicates that dedicated values, e.g. “Min” or “Max”, are expected to be integer values. Take care that statisical measures like “Mean” certainly may be real numbers. If this condition is violated in the description data, a warning will be displayed.

For sequence descriptors the sequence type Nucleodide sequence or Proteine sequence must be selected. Enable ambiguity symbols determines if in the sequence data ambiguity symbols like “S” for “C or G” in nucleotide sequences, are allowed. In case of protein sequences the Symbol length may be chosen from one letter sybols (e.g. “A” for “Alanine”) and three letter symbols (e.g. “Ala” for “Alanine). The Gap symbol is a symbol that indicates gaps of unspecified length and must meet the selected symbol length.

 

Project assignement

Descriptors are not directly assigned to a project, instead descriptortrees are used. One descriptor may be included in several descriptor trees and therefore belong to several projects or it might be unassigned. In both cases dedicated hints will be displayed at the bottom of the application window (see pictures above and below).

You can easily find descriptors that are not included in any descriptor tree by setting “Descriptor tree” → “Assignment” to “Ø” in the search criteria. By opening the Descriptor treetab these descriptors may be easily inserted into a tree by selecting the tree (node) and clicking

If the actually selected descriptor is referenced by more than ony project and not all of the projects can be modified by the actual user, the descriptor data cannot be changed, which will be indicated at the lower right corner of the application window (see above).

 

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Jan 14, 2025

Subsections of Edit Descriptor

Edit Descriptor Modifier

Editing the descriptor - Modifier/Frequency tab

The Modifier/Frequency tab allows definition of modifier and frequency values. The sequence number column (“No.”) determines the display sequence in selection lists. You may order the entries by clicking on a column header. With the arrow buttons ( ) you can move the selected entries up or down within the table, clicking button or shifts the selected entries to the top respective bottom of the table. After ordering the entries click button to renumber the table entries (starting with “1” for the first table entry) and make the changes effective. After pressing button column “Use” shows the number of references in the database for each modifier rsp. frequency value.

To enter a new modifier or frequency value, select the empty line on the end of the table and click on the “Modifier” rsp. “Frequency” field to enter the new values. After entering the new entry name automatically a new value for “No.” is initialized. To delete an entry, select the entry and press the tool strip button, the Delete key or remove the value in the sequence number column (“No.”).

There is a number of predefined modifier and frequency values commonly used. These values can be accessed by pressing the  button, which opens one of the windows shown below.

 

 By checking of uncecking the values, they can easily be inserted or deleted from the modifier rsp. frequency list. Values that are already used in the database are marked by a grey text colour. When these values are marked to be removed from the list, you will be asked for each single value if it really shall be deleted after pressing OK. New values are inserted at the end of the list (see below).

  

You may order the modifier and frequency values according the sequence of the predefined values by pressing the  button, which opens one of the windows shown below. Values that are not in the predefined lists will be shifted to the end of the list.

 

 

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Jan 14, 2025

Edit Descriptor Resources

The resouce links tab allows assigment and inspection of resource links for the descriptor. In the lower Resources part of the tab there are two tables. Ar the left the “Resource” table specifies the single resources, at the right the “Resource variant” table contains the associated URLs to images, video or sound resources.

To enter a new resource select the empty line at the end of the “Resource” table and click on the “Resource name” field. After entering the “Resource name” (leave the cell by pressing the TAB key) automatically a new value for the sequence number (“No.”) is initialized. The sequence number determines the display order in tables and may be changed manually. You may order the resource entries by clicking on the column header or by using the arrow buttons in the left tool strip ( and for up and down, and to shift the selected entry to top or bottom). After ordering the resources click button to renumber the entries starting with “1” and make the changes effective. In field “Ranking” you may enter a numeric value in range 0 … 10 expressing the suitability of the resource. In field “Role” you may select one of the offered values.

If you want to delete a resource, you have three choices:

  1. Select the resource and press the button in the left tool strip.
  2. Select the resource and press the Delete key on the keyboard.
  3. Enter the sequence number column (“No.”) and remove the value. After leaving the cell the entry will be deleted.

In any case you will be asked if you want to delete the data row, if resource links are present. 

To view or edit the additional resource data and copyright information press on the button besides the resource table. In field License: and a link to the license text in the web may be entered, in field Rights: you may enter a copyright text. By pressing the button a browser window can be opened to navigate to the license page in the web. Furthermore you may enter a detailled text (field Details:), the resource language (field Language:) and set the Display embedded flag (see picture below). If any additional resource data have been entered, this will be indicated by a square (□) behind the resource name’s sequence number.

 

To enter a resource link, first select the entry in the “Resource” table, then select the empty line at the end of the “Resource variant table”. By clicking on the “URL” field a web address may be entered. By double-clicking the “URL” field a browser window opens to navigate to the resource. For each resource several URLs to resource variants with different quality levels, e.g. different resolution, may be inserted. For each entry in the URL table a different value of “Variant” must be selected.

As an alternative to a resource URL a colour may be spcified in the format “color://#rrggbb” where “rrggbb” specifies a hexadecimal colour code. The colour can simply be seleced by clicking the button besides the resource variant table.

To remove a resource variant, select the entry and press the button in the right tool strip or the Delete key on the keyboard. Alternatively you may delete the “URL” entry in the resource variant table. 

The button besides the resource variant table allows you to view a resource URL in the system browser.

The upper part of the resource links tab consists of a preview window on the left side and the complete list of resource links. By selecting one of the links the preview is shown on the preview window. If you press button in the preview window, the resource is opened in a separate viewer window.

At the bottom of the resource links tab the media data of a selected URL are displayed. These data can be edited by double-clicking the “Type” entry in the resource variant table, by clicking at one of the media data value fields or the button. The edit dialog provides the possibility to access the URL to get available data. Alternatively the values may be edited manually.   

 

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Jan 14, 2025

Edit Descriptor States

Editing the descriptor - Categorical states tab

The Categorical states tab is only enabled, if the descriptor type has been set to “Categorical”. The upper part of the state tab shows the table of categorical states. To enter a new state select the empty line at the end of the table and click on the “Categorical state” field. After entering the “Categorical state” name (leave the cell by pressing the TAB key) automatically a new value for the sequence number (“No.”) is initialized. The sequence number determines the display order in tables and may be changed manually. You may order the state entries by clicking on the column header or by using the arrow buttons in the tool strip right besides the states ( and for up and down, and to shift the selected entry to top or bottom). After ordering the states click button to renumber the entries starting with “1” and make the changes effective.

If you want to delete a categorical state, you have three choices:

  1. Select the state and press the button in the tool strip right besides the states.
  2. Select the state and press the Delete key on the keyboard.
  3. Enter the sequence number column (“No.”) and remove the value. After leaving the cell the entry will be deleted.

In any case you will be asked if you want to delete the data row. If the categorical state is already used in any description items, the number of affected entries will be shown and you have the option to abort the action. 

If for a state at least one assigned resource is present, the state is marked by a square (□) behind its sequence number (see image above). After selecting the categorical state its assigned resources ar displayed in the lower part of the state tab, the State resource links. It allows management of resources linked to a categorical state marked in the upper table. For a detailled description take a look at the Resource links tab section.

 

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Jan 14, 2025

Edit Descriptor Trees

Editing the descriptor - Descriptor tree tab

The Descriptor tree tab provides the possibility for a structured assignment of the descriptors to the projects. The Descriptor tree consists of three node types, which show the administered projects, descriptor trees, descriptor tree nodes and descriptors. The tree parts’ colours are shown in the example at the bottom. By pressing the button on the tool strip at the right side the example may be hidden. The buttons displayed on the too strip will change depending on the selected entry.

The descriptor trees support three main functions:

  • Assignment of descriptors to a certain project
  • Selection of recommended Frequency/Modifier values and Statistical measures for a certain descriptor
  • Structured arragement of the descriptors, e.g. for hierarchical selection lists and definition of descriptor subsets for description editing and export

 

Descriptor trees are the root of a tree and may only be appended at a project. To insert a new descriptor tree select a project and press . Descriptor tree nodes may be appended at a descriptor tree or another descriptor tree node. To insert a new descriptor tree node, select the parent and press . Descriptors may be appended to a descriptor tree or a descriptor tree node. To append a descriptor select the parent and press , to remove it select the descriptor and press . All these functions can alternatively be accessed by the context menu by a right click on the entry. The descriptor type is indicated by different icons. Categorical descriptors are marked as , quantitative descriptors as , text descriptors as and sequence descriptors as .

You may change the name of a Descriptor tree or a Descriptor tree node in three different ways:

  1. Select the tree element (single click) and then click once on it.
  2. Select the tree element (single click) and click on button in the tool bar on the right.
  3. Right-click the tree element and select item Edit name from the context menu.

You may edit the name of the selected node within the tree. The Descriptor tree must be globally unique. The Descriptor tree node names must be unique with respect to their tree position, i.e. all nodes with the same parent within a descriptor tree must have distinguished names.

If a Descriptor tree or a Descriptor tree node does not contain any other element, it may be deleted by pressing  (delete descriptor tree) rsp. (delete descriptor tree node). Please be aware that in edit mode “Descriptor” the descriptor tree shows only the descriptor that as actually selected in the query panel! To get a complete overview of all descriptors assigned to a certain descriptor tree and to delete trees or nodes with all included objects, select edit mode “Project” (see Editprojects).

If projects and their associated descriptor trees cannot be changed, because the project has been set to “read-only” state, these parts are displayed with grey text color (see project “Schmetterlinge” in picture above).

Descriptor trees can be marked as “tree complete”, to indicate that they should contain all descriptors of the project. In this case the symbol of the descriptor tree changes from to . Setting and resetting the “tree complete” flag is described in the Edit projects section, where additional edit options are availabe.

When a new descriptor tree or descriptor tree node is inserted it gets a numeric name, which may be changed by clicking on the node or selecting from the context menu. Take care that the names of the discriptor trees must be unambiguous within the whole database! The names of the descriptor tree nodes must only be unambiguous within one parent.

If no descriptor tree is installed for a certain project, all descriptors, modifier/frequency values and statistical measures will be usable in the project’s descriptions. Anyway, if you export data or generate documents an do not have an appropriate descriptor tree, you might have missing data! If a project contains several descriptor trees, the available descriptors are the superset of the descriptors assigned to all contained trees.

 

Sorting of descriptor tree elements 

By pressing the button you can expand the tree view to display all elements, by pressing the tree will be collapsed to descriptor tree level. With the arrow buttons ( rsp. ) you can move descriptor tree nodes up or down rsp. to the top or the bottom. An additional ordering option is to select the descriptor tree node you want to move and click the button. The button’s back color changes to red and you may now select the new position in the tree.

In operation mode Edit projects you may take over the descriptor order from a descriptor tree to the descriptor sequence numbers of all project’s descriptors. This will affect the descriptor presentation for description data editing or document generation.  

 

Descriptor tree node details  

For Descriptor tree nodes you may enter an abbreviation a details text and assign resource data. Select the Descriptor tree node (single click) and click on button in the tool bar on the right. Alternatively you may right-click the Descriptor tree node and select Edit details from the context menu. An edit window as shown below will be opened.

If resources are assigned to a Descriptor tree node, its symbol is shown with grey background in the descriptor tree. You may view the resources by right-clicking it and selecting View resources from the context menu.  

 

Recommended statistical measures, modifiers and frequency values 

Click on in the tool bar to close the edit window in the right part of the tab or on  to reopen it. In the edit window you can select recommended modifier/frequency values and statistical measures. The recommended values can be administered for a selected descriptor or for a selected descriptor tree node. In the latter case selected values are inherited by all subordinate nodes, which will be indicated by the background colour if a subordinate node is selected in the descriptor tree. 

To define the available modifier and frequency values and their display sequence, please refer to the Modifier/Frequency tab. The statistical measure values are predefined, nevertheless their display sequence may be modified using the  button (see image above). A form as shown below will appear. With the arrow buttons ( ) you can move the selected entries up or down within the table, clicking button or shifts the selected entries to the top respective bottom of the table. After ordering the entries click button to renumber the table entries (starting with “1” for the first table entry) and make the changes effective.  

The picture below shows an example for a descriptor where the recommended statistical measures Minimum value, Maximum value and Mean are inherited by the superior node.  

For the contained descriptor only additional values may be selected, but the inherited values cannot be de-selected.

 

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Jan 14, 2025

Edit Project

Editing the project

After starting a database query and selecting an entry in the result list the dataset is diplayed in the edit window. In the header area the dataset name and the project language are shown (see picture below). To check dataset changes, click on the button to open the history.

The main project data may be accessed in the first Main attributestab, which is described below. Click on one of the other tabs in the picture below to go directly to the appropriate manual chapter.

img/DD_Project_Main

In DiversityDescriptions a project may be a pure local project or it can be linked with DiversityProjects. By clicking the button above the query window, a new local project is created. For a local project the name can be set freely - as long as it is unambigious within the database - by clicking the  button behind the project name (see image below). By clicking the button you may view the login names that have access to the project.  

If a project is linked with DiversityProjects, the name is fixed to the value set in DiversityProjects. If the name is modified in DiversityProjects, it will change in DiversityDescriptions, too, when the project data are downloaded. The linking of a local project to DiversityProjects is described below in the Cachedprojects section.  

For a linked project some additional buttons are available (see above): With URI you may view the symbolic address of the referred DiversityProjects entry and with you may view the data in DiversityProjects. By clicking the button you may view the login names that have access to the project. With the button you may release the connection to DiversityProjects. I.e. the current project will become a local project.  

  

Main attributes tab

The main attributes tab provides access to a license URI, a short rights text and a detailled project text. The project language can be selected from a list. In field Rights you may enter a copyright text, in field License and a link to the license text in the web may be entered. By pressing the button a browser window can be opened to navigate in the web.

In the Wording field you may enter an alternative project name, which is used for the cache database. When a project has been published in a cache database and it is renamed, this field offers the opportunity to keep the published name. If a project published in the cache database and is renamed, the original project name will be automatically be inserted in the Wording field, if it is empty. Therefore publishing with the old project name will still be possible. To modify the published project name, too, update or remove the Wording entry and re-create the project in the cache database.

With combo box Language you can select the project’s default language. You man change the display and sorting of the entries in the Language combo box from “<code> - <description>” to “<description> - <code>” (and back) by clicking the button . If you need language codes that are not included in the list, click the button. For more details see Edit language codes.

 

Parent project

In the bottom area at the left side the Parent project can be adjusted. If the project has no parent, select “Root” (symbol ). The Parent project adjustment has an influence on the available descriptors, recommended modifier and frequency values and recommended statistical measures, because these adjustments are inherited by the subordinate project. If for a project in the Parent project tree no write access is possible, this is indicated by grey text colour and symbol . The missing write rights for a parent project has no influence on accessability of the actually selected project, except that the parent project adjustment cannot be changed. 

 

Cached projects

The Cached projects section shows entries that are downloaded fromDiversityProjects and not yet used within DiversityDescriptions (see image below, left). Accessible projects are shown with symbol , read-only projects as and projects wihout any access rights as . When you click on the project name, additional buttons are displayed (see image below, right). You may view the database link by clicking on URI or view the data stored in DiversityProjects by clicking on symbol . By clicking the button you may view the login names that have access to the project. With button you may link the current project to the selected DiversityProjects entry.

            

 

Scope values

In the Scope values section at the right the values for scope types “Sex”, “Stage” and “Other scope” may defined. When you mark one of the entries, a tool strip with the available operations is shown at the right border of the control. To insert a new value, select the scope type and press button . In case of “Sex” one of the predefined “sex status” values derived from the SDD standard has to be selected. In all other cases a new value with a numeric key is appended, that can be renamed by pressing the button and selecting Edit scope name or by clicking at the name. 

In case of “Sex” scope the “Edit” menu offers the additional menu items Reset scope name, which appears if the name differs from the original “sex status”. Further the “sex status” value may be changed with menu item Set sex status. For the other scope types you may enter a details text by pressing the button and selecting Edit scope details.

To remove a scope value, select it and press the button. To make a value available for the project, the check box must be checked. If the selected project has a parent and a value has already been checked in the parent project, this is indicated by the background colour (see image below).

 

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Jan 14, 2025

Subsections of Edit Project

Edit Project Dependencies

Editing the project - Descriptor applicability tab

The Descriptor applicability tab serves the administration of dependencies between categorical states and dependent descriptors. First a descriptor has to be selected either by its name in the alphabetically ordered drop down list or its sequence number (“No.”) in the first line of the descriptor dependencies tab. If for the selected project a descriptor tree is present, the  button allows selecting the descriptor form the descriptor tree (see picture below). 

The table Controlling states in the upper left part of the tab shows the categorical states if a categorical descriptor has been selected. When you have adusted the restrichted descriptor view, visible by the button in the toolbar of the Dependent descriptor section, only the actually set dependent descriptors are displayed here. You can switch to an alternate Full descriptorview as described below. For each categorical state Dependent descriptors can be inserted by pressing the button. A dialog window opens to select the descriptor either by its name, sequence number or using the descriptor tree (see picture below).

 

In column “Rule” the symbol indicates that the dependent descriptor is inapplicable if the controlling state is present in a description. The symbol indicates that the controlling state must be present in a description if the controlled descriptor shall be applicable. The rule can be toggled by clicking the symbol in the table or by pressing the corresponding button ( rsp. ) at the right. To remove a dependent descriptor select it and press the button.

In the lower part of the tab you find the States controlling this descriptor. You may double-click on the item to select navigate to it for editing. Alternatively you may edit the controlling descriptor states using the control buttons of the tool strip at the right. By double-clicking an entry in Dependent descriptors or in States controlling this descriptor you may navigate forwards and backwards in the chain of dependent descriptors.

If you want to get an overview of all the project’s descriptor dependencies or want to delete all dependencies, take a look at the Applicability tree section below.

 

 

Calculation of the descriptor applicability

To decide if a descriptor is applicable in a description, the following conditions are evaluated:

  • Inapplicable-if rule: If only controlling states are present in a description, these make the controlled descriptor inapplicable. The character remains applicable if either no state at all, or any non-controlling states are present.
  • Applicable-if rule: If any controlling state is present in a description, these make the controlled descriptor applicable. It is inapplicable if only non-controlling states are present.
  • Special condition 1: If the controlling descriptor is inapplicable (through another applicability rule, or through an explicit “Not applicable” data status value), the controlled descriptor is always inapplicable as well.
  • Special condition 2: If no data for the controlling descriptor are present in a description (data completely missing or only status is “Missing data” or “Not to be recorded”), the controlled descriptor always remains applicable.

 

 

Full descriptor view

By clicking the button in the toolbar of the Dependent descriptor section, you can chenge to the full descriptor view (see image below). In section Dependent descriptors all available project descriptors are shown. You may set a dependency by selecting the descriptor and clicking the button rsp. . To remove the dependency, click on button . Alternatively you may click on they symbol in the table column “Rule” to change the values in the sequence -> .

If you select a values for the Descriptor tree, the descriptor list is restricted to the values included in that descriptor tree. Please be aware that existing dependencies might be hidden by such a selection! 

You can return to the restricted descriptor view by clicking on button .

 

 

Applicability tree

Instead of the States controlling this descriptor you may display a complete overview of the descriptor applicability rules by pressing the button in the Dependent descriptors section (see image below). By double-clicking an item in the Applicability tree you can open it for editing.

By pressing the button in the Applicability tree section you can delete all dependencies shown in the tree.

 

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Jan 14, 2025

Edit Project Modifier

Editing the project - Modifier/Frequency tab

The Modifier/Frequency tab allows definition of modifier and frequency values. The sequence number column (“No.”) determines the display sequence in selection lists. You may order the entries by clicking on a column header. With the arrow buttons ( ) you can move the selected entries up or down within the table, clicking button or shifts the selected entries to the top respective bottom of the table. After ordering the entries click button to renumber the table entries (starting with “1” for the first table entry) and make the changes effective. After pressing button column “Use” shows the number of references in the database for each modifier rsp. frequency value.

To enter a new modifier or frequency value, select the empty line on the end of the table and click on the “Modifier” rsp. “Frequency” field to enter the new values. After entering the new entry name automatically a new value for “No.” is initialized. To delete an entry, select the entry and press the tool strip button, the Delete key or remove the value in the sequence number column (“No.”).

There is a number of predefined modifier and frequency values commonly used. These values can be accessed by pressing the  button, which opens one of the windows shown below.

 

 By checking of uncecking the values, they can easily be inserted or deleted from the modifier rsp. frequency list. Values that are already used in the database are marked by a grey text colour. When these values are marked to be removed from the list, you will be asked for each single value if it really shall be deleted after pressing OK. New values are inserted at the end of the list (see below).

 

You may order the modifier and frequency values according the sequence of the predefined values by pressing the  button, which opens one of the windows shown below. Values that are not in the predefined lists will be shifted to the end of the list.

 

 

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Jan 14, 2025

Edit Project Move Trees

Editing the project - Move or copy descriptor trees

Using the context menue, you may move or copy parts of a descriptor tree to other branches. Please note that for the move and copy operations the selected project, marked by its background colour in the descriptor tree, is assumed as the target project. You may copy descriptor trees or parts of projects with read-only access to your selected project. The move operation is certainly not possible in those cases. Note that by the copy operations only the tree structures will be copied, associated recommended statistical measures, modifiers and frequencies will not be copied! The move operations preserve those adjustments.

Remark: If you want to move or copy element from an other than the selected project, activate the “Show all projects” option by clicking the button in the tool strip. The icon background will be changed to red color to indicate that this option is active.

1. Move or copy a descriptor tree

Right click on the descriptor tree you want to move/copy. A context menu opens, that offers the options Copy ‘<tree name>’ to ‘<project name>’ rsp. Move ‘<tree name>’ to ‘project name’ (see picture below left). If you selected “Move”, the descriptor tree is removed from the original project and appended to your selected project. If you selected “Copy”, a copy of the tree will be appended to the selected project. In this case numeric IDs are appended to generate unique tree and tree node names (see picture below right). The copy function can be used to generate a clone of a descriptor tree in the selected project.

  

Additionally you may copy the contents of a descriptor tree to a descriptor tree node by clicking selecting the option Copy descriptor tree to descriptor tree node … rsp. Move descriptor tree to descriptor tree node … (see picture above left). A separate window opens to select the target node (see picture below left). Find the move result in the right picture below. Since the tree has been moved, the tree node names have not been changed. One duplicate descriptor has not been moved to the target node. 

   

2. Move or copy a descriptor tree node

Right click on the descriptor tree node you want to move/copy. A context menu opens, that offers the options Copy descriptor tree node … rsp. Move descriptor tree node … (see picture below left). After selecting one of there items a dialog windows opens where you may select the target descriptor tree or descriptor tree node (see picture below right).

   

If you selected “Move”, the descriptor tree node is removed from the original position and appended to the selected tree position. If you selected “Copy”, a copy of the tree node will be appended to the selected tree position. In this case numeric IDs are appended to generate unique tree node names (see picture below). The copy function can also be used to generate a clone of a descriptor tree node in the selected project.

3. Move or copy a descriptor

Right click on the descriptor you want to move/copy. A context menu opens, that offers the options Copy descriptor … rsp. Move descriptor … (see picture below left). After selecting one of there items a dialog windows opens where you may select the target descriptor tree or descriptor tree node (see picture below right).

 

If you selected “Move”, the descriptor is removed from the original position and appended to the selected tree position. If you selected “Copy”, a new descriptor node will be appended to the selected tree position (see picture below).

 

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Jan 14, 2025

Edit Project Trees

Editing the project - Descriptor tree tab

The Descriptor tree tab provides the possibility for a structured assignment of the descriptors to the projects. The Descriptor tree consists of three node types, which show the administered projects, descriptor trees, descriptor tree nodes and descriptors. The tree parts’ colours are shown in the example at the bottom. By pressing the button on the tool strip at the right side the example may be hidden. The buttons displayed on the too strip will change depending on the selected entry.

By default only the selected project. its subordinated projects and their descriptor trees are displayed. You may select the “Show all projects” option by clicking the button in the tool strip to show alle projects. To indicate that this option is active, the icon background will be changed to red color (see images below). Be aware that this option might slow down data loading.

The descriptor trees support three main functions:

  • Assignment of descriptors to a certain project
  • Selection of recommended Frequency/Modifier values and Statistical measures for a certain descriptor
  • Structured arragement of the descriptors, e.g. for hierarchical selection lists and definition of descriptor subsets for description editing and export

Descriptor trees are the root of a tree and may only be appended at a project. To insert a new descriptor tree select a project and press , to delete it select the descriptor tree and press . Descriptor tree nodes may be appended at a descriptor tree or another descriptor tree node. To insert a new descriptor tree node, select the parent and press , to remove it select the descriptor tree node and press . Descriptors may be appended to a descriptor tree or a descriptor tree node. To append a descriptor select the parent and press , to remove it select the descriptor and press . All these functions can alternatively be accessed by the context menu by a right click on the entry. The descriptor type is indicated by different icons. Categorical descriptors are marked as , quantitative descriptors as , text descriptors as and sequence descriptors as .

You may change the name of a Descriptor tree or a Descriptor tree node in three different ways:

  1. Select the tree element (single click) and then click once on it.
  2. Select the tree element (single click) and click on button in the tool bar on the right.
  3. Right-click the tree element and select item Edit name from the context menu.

You may edit the name of the selected node within the tree. The Descriptor tree must be globally unique. The Descriptor tree node names must be unique with respect to their tree position, i.e. all nodes with the same parent within a descriptor tree must have distinguished names.

If projects and their associated descriptor trees cannot be changed, because the project has been set to “read-only” state, these parts are displayed with grey text color (see project “Schmetterlinge” in picture above).

When a new descriptor tree or descriptor tree node is inserted it gets a numeric name, which may be changed by clicking on the node or selecting from the context menu. Take care that the names of the discriptor trees must be unambiguous within the whole database! The names of the descriptor tree nodes must only be unambiguous within one parent.

If no descriptor tree is installed for a certain project, all descriptors, modifier/frequency values and statistical measures will be usable in the project’s descriptions. Anyway, if you export data or generate documents an do not have an appropriate descriptor tree, you might have missing data! If a project contains several descriptor trees, the available descriptors are the superset of the descriptors assigned to all contained trees.

 

Editing the project descriptor assignemnts for a tree node 

When you use button to append a descriptor to a tree node, you will be offered all accessible descriptors in the database. In many cases, when you have already assigned all required descriptors to the project, you may wish to build some additional structured descriptor trees. If you select a descriptor tree or a descriptor tree node, the button is shown (see image below left). After clicking this button you will get a selection list with all descriptors assigned to the project. Descriptors that are included in the tree node are selected in the list (see image below right). You may easily change the selection and click “OK” to make the changes effective.

 

Sorting of descriptor tree elements 

By pressing the button you can expand the tree view to display all elements, by pressing the tree will be collapsed to descriptor tree level. With the arrow buttons ( rsp. ) you can move descriptors or descriptor tree nodes up or down rsp. to the top or the bottom. An additional ordering option is to select the descriptor tree node you want to move and click the button. The button’s back color changes to red and you may now select the new position in the tree. If you select a descriptor tree or a descriptor tree node, you may arrange the contained descriptors in alphabedical order by clicking the buttons (ascending) or (descending).

A descriptor tree may be marked as “tree complete” to indicate that this tree shall contain all descriptors for the project. This is done by selecting the descriptor tree node and clicking the button . To indicate that the tree is marked as complete the tree icon changes to (see picture below). 

The “tree complete” flag may be removed by clicking the button and the tree icon will be changed back to (see picture below).

  

If a descriptor tree is marked as “tree complete”, it can be used to take over the sorting of the descriptor nodes to the sequence number of the descriptors. But you must be aware that the descriptor’s sequence number (field “No.” in “Edit descriptor” main panel) is not project or tree dependent, i.e. that this operations will have influence on the dispolay sequence of all descriptions using these descriptors. Click on button (see picture above) to open the descriptor sorting window below.

The first column shows the descriptor names as sorted in the descriptor tree, the second column shows the current sequence number int the database and the last column shows the new sequence number. If the sequence number stays unchanged, the new sequence number is displayed with green background, otherewise with yellow background. You may click on a new sequence number and change its value manually. By clicking on the table headers, you may sort the table display according descriptor names, old or new sequence numbers. If a descriptor may not be changed, because it is assigned to a project where the user has no write access, the whole line is displayed with grey backgound and cannot be changed. Finally click on OK to accept or Cancel to reject the changes. 

An additional option available for complete trees is to copy missing descriptors with button . The descriptors available for a certain project include all descriptors assigned to all descriptor trees of the project and its sub-projects. In our example a new descriptor tree has been assigned to the upmost project (see image below left). After clicking the button all valid descriptors are inserted to the descriptor tree (see image below right). 

 

 

Descriptor tree node details  

For Descriptor tree nodes you may enter an abbreviation a details text and assign resource data. Select the Descriptor tree node (single click) and click on button in the tool bar on the right. Alternatively you may right-click the Descriptor tree node and select Edit details from the context menu. An edit window as shown below will be opened.

If resources are assigned to a Descriptor tree node, its symbol is shown with grey background in the descriptor tree. You may view the resources by right-clicking it and selecting View resources from the context menu.  

 

Click on in the tool bar to close the edit window in the right part of the tab or on  to reopen it. In the edit window you can select recommended modifier/frequency values and statistical measures. The recommended values can be administered for a selected descriptor or for a selected descriptor tree node. In the latter case selected values are inherited by all subordinate nodes, which will be indicated by the background colour if a subordinate node is selected in the descriptor tree.  

To define the available modifier and frequency values and their display sequence, refer to the Modifier/Frequency tab. The statistical measure values are predefined, nevertheless their display sequence may be modified using the  button (see image above). A form as shown below will appear. With the arrow buttons ( ) you can move the selected entries up or down within the table, clicking button or shifts the selected entries to the top respective bottom of the table. After ordering the entries click button to renumber the table entries (starting with “1” for the first table entry) and make the changes effective.  

The picture below shows an example for a descriptor where the recommended statistical measures Mini mum value, Maximum value and Mean are inherited by the superior node. 

For the contained descriptor only additional values may be selected, but the inherited values cannot be de-selected.

 

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Jan 14, 2025

Edit Sample Data Grid

Sample data grid view

After starting a database query for descriptions select Grid → Sample data grid view … from the menu. The query result list is passed to the description grid view form and a window as shown below opens. In the first line the database name is displayed. If you move the mouse cursor over the database name, a tooltip shows the actual connection paramter.

img/DD_Description_Main

The table in the lower parThe table in the lower part of the window shows the sampling unit IDs in the first column and the sample data in the other columns. Each sample column holds the data of a certain descriptor. The upper part of the window shows the selection parameters that are used for building the sampling unit table. You may change the table colors by clicking the button . A form as shown below will be opened. 

Click on buttons categorical, quanitative, text or sequence to select the corresponding table colors. By clicking the Reset button below the color, the corresponding default value will be selected. After changing the table colors by a click on the OK button, you must re-draw the table.

 

Selection parameters

In the upper left part of the parameters for the samping unit table can be adjusted. If in the query list passed to the form descriptions of different projects are present, the displayed project can be selected with the Project drop-down box. The entries in the drow-down list include the project name, followed by the number of descriptions for that project in brackets and an asterisk (*) if the user has only read access for that project.

After selecing a project in section Descriptions and sampling events (right upper part of the window) the descriptions and their sampling events are listed. Here you may select the descriptions and sampling events that shall be used for building the sampling unit table. The buttons all, none and swap can be used to change the selection of all tree elements. By pressing the button the tree view may be expanded to display the contained sampling events, by pressing the button only the descriptions will be shown. In the bottom of the section the currently selected number of sampling events and sampling units is displayed.

When you click on a single sampling event and more than one description is in the list, the button appears in the tool strip. By clicking this button you can open a description selection window and thus shift the sampling event to a different parent description. 

The Descriptor tree drop-down box restricts the descriptor columns to the descriptors contained in the selected tree. Furthermore the tree hierarchy is included in the descriptor names if a structured descriptor tree is selected (see images below).

  

The values From descriptor and to descriptor limit the range of descriptor sequence numbers that is included in the discription tabe. Be aware that this restiction is additionally effective to a selected desriptor tree! If you want to de-activate this restriction, select “from” value 0 “to” value 999999 by a double-click on the labels From descriptor rsp. to descriptor. The limitation of the number of descriptor columns makes speeds up the description table generation, especally if many descriptor (e.g. some hundrets) are present.

Finally click the button Display sampling units table to build a new sampling unit table according to your settings. During output of the sampling unit table the icon of the button changes to  and you may abort processing by clicking the button.

 

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Jan 14, 2025

Subsections of Edit Sample Data Grid

Edit Sample Data Grid Editing

Sample data grid view - Data editing

The first column of the sampling unit table shows the sampling unit IDs titles, which are fixed. I.e. if you scroll the sample data to the right, the IDs are still visible at the left. The other columns show the sample data, where the descriptor type is indicated by the background colour: categorical, quantitative, text or sequence. The column titles include the descriptor name, the mesurement unit in square bracket for quantitative descriptors and the descriptor’s sequence number (see image below).

When a sample cell in the sampling unit table is selected, the field Sampl. event: shows the sampling event titles, field Description: shows the description title and field Descriptor: shows the symbols according the descriptor type ( for categorical, for quantitative, for text and for sequence) and the descriptor title. If for a descriptor resources are available, this fact is indicated by a coloured symbol background. You may view them by a double-click on the descriptor title. If for a description resources are available, the symbol is displayed before the title. Double click in that symbol to view the resources.

For the selected cell the sample data may be edited as described in section Editing the description - Sample data tab of this manual. For modified sample cells the text colour changes to blue and the sample unit IDs will be shown with yellow background in the table.

 

Changing the sampling event

To shift samling units to a different sampling event, select the whole data rows by clicking in the area left from the “Sampling unit ID” column. In the tool strip the set event button appears. After clicking the button a window for selecting the new parent sampling event will be opened (see image below).

 

Copy sampling units

To copy one or more sampling units select the whole data rows by clicking in the area left from the “Sampling unit ID” column. In the tool strip the copy button appears (see image below).

  

After clicking the button the copied line are inserte at the end of the tabel (see image below). 

  

 

Delete sampling units

To delete one or more sampling units select the whole data rows by clicking in the area left from the “Sampling unit ID” column. In the tool strip the copy button appears.

 

New sampling unit

To enter a new sampling, click on button and a new row will be appended. After clicking the button a window for selecting the sampling event will be opened.

  

 

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Jan 14, 2025

Edit Sample Data Grid Save

Sample data grid view - Save or discard changes

When you click in button “OK” the sample data grig view is closed and all changes are automatically saved in the database. If you did some changes and want to save them without leaving the form, simply click on (see image below). If you close the window, e.g. by clicking the “Cancel” button, and still have unsaved changes, you will be asked to save or discard the changes.

img/DD_Description_Main

 

Undo all changes

You may discard all unsaved changes without leaving the form by clicking the button and the data will be reloaded form the database (see image below). 

  

 

May 3, 2024

Table Editors

Table editors

For the data selected in the main window the table editors offer a direct access to the tables of the database. Underneath the menu Grid  select one of the Table editors. 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. The following tables are included for direct access:

Depending on the edit mode the following options are available in the Table editors menue:

  • Edit descriptions
    • Sampling events to edit the sampling events of the descriptions in the query result list
    • Descriptions to edit the descriptions in the query result list
    • Description resources to edit the resource entries for the descriptions in the query result list
    • Resource variants to edit the resource variant entries for the descriptions in the query result list
    • Translations to edit the translation entries for the descriptions in the query result list
  • Edit descriptors:
    • Descriptors to edit the descriptors in the query result list
    • Descriptor resources to edit the resource entries for the descriptors in the query result list
    • Categorical states to edit the categorical states of the descriptors in the query result list
    • Categorical state resources to edit the resource entries for the categorical states of the descriptors in the query result list
    • Resource variants to edit the resource variant entries for the descriptors and categorical states in the query result list
    • Translations to edit the translation entries for the descriptors and categorical states in the query result list
  • Edit projects
    • Project to edit the projects in the query result list
    • Descriptor tree node resources to edit the resource entries for the descriptor tree nodes of the projects in the query result list
    • Resource variants to edit the resource variant entries for the descriptor tree nodes of the projects in the query result list
    • Translations to edit the translation entries for the projects in the query result list

 

As an example see below the table editor window for projects.

 

Read-only

If for parts of the query result no write access exists, the table editor will be opened in read-only mode. Especially for descriptors you should keep in mind that they may belong to more than one project. Therefore the table editors for descriptors, categorical states and their resources or resource variants may be opened for read-only, if you have not write permissions for all projects in the database. 

 

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.

If you want to delete a line in the database, select it by clicking in the space before the line and press the button. Take care that an undo of that action is not possible.

 

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. If you do not want to save your changes, click on the button to close the window without saving.

 

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.  

Jan 14, 2025

Text Editing

Extended text editor

In the most text fields you can open an extended text editor by double-clicking the text field, which provides the following features:

  • Perform basic text formatting
  • Show and convert RTF-like text formatting
  • Insert and view links to HTML pages or Diversity Workbench database entries

 

Text formatting

In the text fields you may use some HTML mark-ups <b>bold</b> <i>italic</i> and <u>underline</u> for text formatting (see image below left). Additionally the tags <br>, <br/> or <br /> may be inserted to indicate a new text line, but the most common way is to press the ENTER key instead. The format tags will have an effect if documents are generated from the database.

   

By double-clicking the text field you can open a separate edit window that shows the text formatting (see image above right). You can easily change the formatting by selecting a text and clicking the buttons B, I or U.

To reload the original text into the edit window click the button. By clicking OK the changes are taken over to the text field, to ignore the changes, click the cancel button.

 

RTF-like text formatting

In some projects RTF-like mark-ups are used to indicate text formatting, e.g. \iitalics\i0{} for italics. If you double-click on the text field you can open the separate edit window and button indicates that RTF-like format mark-ups have been detected (see image below).

<

By clicking the button the edit window will show you the formatted text (see image below left). After clicking OK the text will be stored using the HTML mark-ups, which is the standard for DiversityDescriptions (see image below right).

  

 

You may open an internet browser by clicking the button . After navigating to your target page, click OK to insert the link at the current cursor position. By clicking the drop-down button you can select a Diversity Workbench database and search for a certain database entry (see image below).

After selecting a found entry and clicking OK the database link is inserted at the current cursor position (see image below). 

When the link is clicked either the web browser opens (for regular HTML links) or the Diversity Workbench application to display the databease entry (see image below).