Diversity Collection

Data handling

The controls for handling data sets in the database are located in the left upper part of the window as shown in the image below. A step-by-step introduction for the creation of new data sets is provided in the Tutorial.

• To SAVE the changes in a data set click on the button. If you select another data set from the list of results, the current changes will be saved automatically.
• To UNDO the changes in a data set, click on the button. This will recover the original data unless the changes have been saved or changes were done in certain tables or hierarchies were the data must be stored to display the hierarchy.
• To create a NEW entry in the database click on the button. This will create a new record of a specimen and show it in the list of results.
• To COPY the data of a specimen record choose it from the list and click on the button. For further details, see the chapter Copy specimen.
• - To DELETE a data set you must have the proper rights (e.g. be a member of the group Administator). Select the dataset you want to delete it in the list and click on the button.

To delete all selected specimen choose Data - Remove specimen... from the menu. A window as shown below will open where you can choose if the data from the log and the collection events should be included in the removal.

Diversity Collection

Copy specimen

For an introduction see a short tutorial . To copy specimen click on the button. A window will open where you can choose several options for your copies.

In the first tab choose in which way the CollectionEvent - if present - for the new data sets should be created (see image below). In the first option the new specimen will be located in the same collection event as the original dataset. In the second option a new collection event copied from the original will be created while in the last option the data in the collection event will be ignored altogether. 

In the Accession number tab you can search for or enter the accession number you wish to use for your new data set (see below).

In the Projects tab you can add additional projects for you new datasets (see below).

In the Relations tab you can add relations between the original dataset and the copy in either direction (see below).

In the Include... tab you can choose the ranges of data that should be included in the copy (see below). Click on the All or None buttons to select all resp. none of the tables.

In the Number of copies tab you can specify the number of copies. If you checked Create an accession number for the new data set, the program will list all accession numbers which will be created (see below). After you changed the number of copies, click on the button to refresh the list.

 If you do not wish to create new accession numbers for the copies the list will not be shown (see below).

Copy event

If only the event data should be copied and a selected specimen should be transferred into the new event you can choose the last option (see below). This option is only available for events containing several specimen.

Diversity Collection

Tree for the specimen

The upper tree in the window provides an overview for all the data linked with the specimen. With the buttons in the left panel you may hide or show certain nodes in the tree. If for example you do not wish to see the collectors, simply click on the button and they will be hidden in the tree. The button will change to a grey version and the background will turn yellow to show that there is hidden data of the collectors.

If the CollectionEvent is part of a CollectionEventSeries, a drop-down button will appear where you may select between 3 states:

• = show the parent EventSeries
• = show the entire hierarchy of the EventSeries
•     = hide the EventSeries
•     = hide the EventSeries

If the CollectionEvent is linked to a SamplingPlot, a drop-down button will appear where you may select between 3 states:

• = show the parent SamplingPlots
• = show the entire hierarchy of the SamplingPlots
• = hide the SamplingPlots
•     = hide the SamplingPlots

If both options are available, you may choose between the CollectionEventSeries or the SamplingPlot hierarchy. If the entire hierarchy for the EventSeries or the SamplingPlots is displayed, the items not included in the current data set will be displayed with gray icons, e.g. . To change to one of these use the button. For the Events, the EventSeries, the Plots and the Specimen a button will appear which will give you access to a taxon list of the selected item.

The panel on the right side of the tree is used for editing the data, for example the button will insert a new collector. For further details see the special sections. For data with [Read only] access these panels are disabled except the button for adding annotations . 

Diversity Collection

Display order

Tutorial:

The display order defines the sequence in which the units within this specimen will appear on e.g. a label. The first unit will be printed in the header of the label, others are included in the text below. You can change the display order by using the   buttons. If a unit should not appear on the label, transfer it to the hide list using the  button. The  button returns it to the list to be shown on a label. The first unit can not be transferred to the hide list.

The upper section shows the display orders of the units within the whole specimen. The lower section shows the display orders in a specimen part. If you print a label without reference to a part, the display order for the entire specimen as in the upper section will be used. This part is also accessible if you click on the button in the right panel of the upper tree, which will appear if you e.g. select the specimen.     

If you print a label with reference to a part, the display order for the part as in the lower section will be used. This area will be shown when you select a specimen part in the lower tree. In addition to the display order you can specify whether an organism is present in a selected part of a specimen. With the button you can transfer all organisms into the part.

To change the sequence of the parts according to e.g. the name instead of setting all entries one by one, you may choose among the options shown in the image below (Name, Identifier, ID).

Diversity Collection

Accession

The accession of a specimen in a collection is documented with its accession number and the date of the accession if available.

If the specimen was received from another collection, this may be documented with the name of the depositor and the number in the original collection (Dep.Nr).

If the current project (= as selected in the query list) contains a duplicate of the accession number, a button will appear. This gives you the opportunity to switch to the specimen with the duplicate accession number.

If a new specimen is entered you can use the button to search for the next free accession number. A window will open as shown below, where you can begin the search. The search will start with the number you provide as a starting point. 

The system will try to find the next free number based on the accession numbers available in the database. As accession numbers can be assigned to a specimen as well as a part of a specimen, you have the option to include accession numbers in both places in the query. Click OK to use the recommended number for the specimen.

Data concerning the accession and deposition are stored in the table CollectionSpecimen.

Diversity Collection

Specimen image

To see the specimen images select the specimen image in the header menu. Each specimen may be documented with several images. The images are stored as their path, either locally or provided by a server. To enter a new image click on the button. For more details see the section Images.

To delete an image select it from the list and click on the button (see below).

To change the sequence of the images, use the resp. buttons to change the position of the selected image. To adapt the sequence of the whole list, you can select one of the options offered when you click on the button: Ordering ascending resp. descending by the name (= URI) or the creation date of the images. For a short introduction see the tutorial .

With the button you can change to a new chromium based browser for the display of images.

To change the image sequence for a whole project, use the functionality within maintenance maintenance.

To document the relation of an image to an organism or a part of the specimen choose the corresponding entries from the drop-down lists Organisms: and/or Part:.

To restrict the displayed images to either images which are related to a certain part or a certain organism within the specimen, choose e.g. the organism in the tree. If the selected organism is related to any image the button (see below) will change to .  

Click on the button to restrict the images displayed in the list to those, which are related to e.g. the selected organism. The button will receive a red background to remind you of the restriction. Next to the image list a button will appear which enables you to show all images again.

The data is stored in the table CollectionSpecimenImage.

Diversity Collection

Projects

	Setting of projects	Effect on specimen within Projects
	Full access to all projects	User can edit data
	Any project read only	User can read data
	Any project locked	No user can edit data
	No access to project	User cannot see data

Every CollectionSpecimen may be assigned to any number of projects. To assign a specimen to a project click on the button. To add a project where you have no access to, use the button. To remove a specimen from a project select the project from the list and click on the button.

If there are projects, to which you have [no access] to, these will be listed in a separate list at the top as shown below.

Projects, to which you have Read only access will be listed in a separate list at the top as shown below.

Data from Read only projects can be seen but not edited. Only Annotations can be added (see image below).

To transfer all selected specimen into an additional project choose Data → Transfer → To project... from the menu. A window will open where you can select the project to which the specimen should be added.

To remove all selected specimen from an additional project choose Data → Remove from project... from the menu. A window will open where you can select the project from which the specimen should be removed. The last project in which a specimen is placed can not be removed.

The data are stored in the table CollectionProject.

Details of the projects within the DiversityWorkbench are stored in the database DiversityProjects. To access further information on a project click on the button. To edit details in projects you require the application DiversityProjects.exe in your application directory and access to the database DiversityProjects. To synchronize the projects listed in DiversityProjects you may use the synchronize function in the useradministration window as shown below. If DiversityProjects is not available, you may create a new project by clicking the button. If DiversityProjects is available, use the synchronize function .

To import new projects from the DiversityProjects, select Administration - Projects from the menu. A window as below will open where the available projects are restricted to the type "Collection" . (Short introduction: )

To select a project of a different type or missing type, deselect the restriction (see below).

The present project list details about the projects available in DiversityCollection.

the diagram below shows all tables with direct relations to the project tables. For more details see the sections Analysis, Processing and Image description.

Diversity Collection

Notes and problems

To enter notes or problems connected with the specimen select it in the hierarchy. The data form will open the corresponding fields. The Original notes are the notes found on the label of the specimen, made by the original collector or from a later revision. Additional notes are those made by the editor of the specimen record, e. g. doubtful identification or locality.

In the Problems area enter the description of a problem which occurred during data editing. Typically these entries should be deleted after help has been obtained. Do not enter scientific problems here. Use Additional notes for such permanent problems!

The data is stored in the table CollectionSpecimen.

For notes on data created by users with no permission for editing see the chapter Annotation.