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

Editing the descriptor - Resource links tab

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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