Diversity Collection

Grids

To edit the data in a data grid, select Grid mode for the specimen , the organisms , the parts , the images the collection events or the collection event series from the menu. A window will open where each dataset from the query result list is represented in a single line for a specimen, an organism, a CollectionEvent or a CollectionEventSeries respectively. Please note that in this view, only a limited part of the data is visible. For example, only the most recent identification of an organism is displayed. This is shown in the image below, where two organisms (marked with red arrows) are not visible in the grid view because only the latest identification per organism is shown.

When using grid mode for organisms, all organisms will appear, but only with their most recent identification.

Customise column headers

The names of the columns can be changed using the database description.

Customise fiel visibility

The selection of the visible fields can be adjusted in the tree above the list. Change the selection of the columns and click on the Set columns button.

Customise column width and sequence

To adjust the width of the columns or the height of the rows, either drag the border with the mouse or double-click on the border to obtain the optimum size for a column. You can also click the button for the optimal height of the rows or the button for the optimal width of the columns. To change the width and sequence of the columns, drag the columns to the position of your choice or adjust the width to your preference. These changes will be saved for this session and the next time you use grid mode. To return to the original sequence of the columns, click the Reset sequence button.

Sorting the data

To sort the data in the grid, click in the header of the column you want to use as the sorting column. The sort will persist even if you change values in that column. This means that if you change a value in the sort column, the changed record will be placed in the new position according to its new value. The sorting of a column is indicated by an arrow indicating the direction of sorting (up or down) and by a thicker right margin of that column (see image below).  

Find and replace

To use the find and replace functions, you must either select part of the field in this column or click the button to select the whole column. You can then select the function you wish to use (remove, insert, append or replace). To replace a part of the text in the selected fields, type the text to be replaced and type the replacement in the appropriate fields. To start the replacement, click on the button. To insert a string to the beginning of all entries in the selected fields, click the button. To append a string to all entries in the selected fields, click the button. To remove all entries from the selected fields, click the button.

Transfer from spreadsheet

You can transfer data from a spreadsheet, such as Excel or Calc. Copy the relevant columns from your spreadsheet and paste them into DiversityCollection. Click in the top-left cell where the data should be inserted, then open the context menu (click the right mouse button) and select Insert to paste the data.

Editing

Some columns cannot be edited directly, but are linked to external modules or services. These columns are displayed as buttons. Click on the button to access the service. If a value is linked to an entry in an external module, the background will change to [yellow], and the text will no longer be editable.

Together with the links (as shown in the example above [Link to DiversityAgents]), you can also select columns that allow you to remove links to modules (e.g. [Remove link for collector] in image above). These columns appear as buttons . Simply click on the button associated with a link to remove the connection to the corresponding module. After doing so, you can edit the text field containing the previously linked value.

Some values are linked to a predefined list of options. To change such a value, use the drop-down list available in the column.

New dataset

If you click on the empty line at the base of the data grid, you will be asked if you wish to create a new dataset. The program will ask you for a new accession number and the project of the new dataset. Another way to create a new dataset is to use the copy button . Simply click on the row you wish to create a copy of and then click on the copy button . For details see the Data section. A copy of the dataset will be inserted at the base of the data grid.

Saving the data

To save all changes, click the button. To undo all changes since the last time the datasets were saved, click the button. To save the changes to the current dataset use the button. To undo the changes in the current dataset, click the button. If you click the OK button, you will be asked if you want to save the changes before the window closes. If you click the Cancel button or close the window, your changes will not be saved. To export the data displayed in the grid as a text file with tabs as column separators, click on the button. 

Diversity Collection

Table Editors

For the data selected in the main window the table editors offer a direct access to the tables of the database as shown in the image below. In the hierarchy tree of the main window every entry corresponds to a table in the database, marked for the image below for the tables CollectionEvent and IdentificationUnit. Underneath the menu Grid select one of the Table editors (see below). For an introduction see a short tutorial .

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. If you are using the optimzed query certain columns that are linked to lookup tables show the translated content instead of the IDs. With the [ ID ] button you can change back to the original, not translated content of the table. The tables below are examples for those that are included for direct access via a table editor:

• Collection events
• Collection event localisations
• Collection event site properties
• Specimens
• Collectors
• Specimen images
• Organisms
• Identifications of the organisms
• Analysis of the organisms
• Specimen parts
• Processings of the specimen parts
• Transactions of the specimen

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

With the button you can set the widths of the columns according to the header and the content. With the button the width is set to the content. After the column width is set, this will be indicated with a yellow background . Click again on the button to release the setting of the column width .

  For more details see chapter TableEditor

Diversity Collection

Spreadsheets

The program provides several spreadsheets with different focus:

• Event
  • Main table: CollectionEvent
  • The focus is the collection event
• TK25
  • Editing data that are linked to a TK25 entry.
  • The sheet provides a link to distribution maps with the option to select data via these maps
• Organism
• Mineral
  • Focus on mineral specimen
• Part
• Collector
  • Main table: CollectionAgent
  • All collectors of a specimen
• Image
  • Main table: CollectionSpecimenImage
  • All images of a specimen
• Analysis
  • Main table: Analysis
  • Administration of the analysis

The spreadsheets similar to the grids provide a tabular access to the data. In addition you can search and filter data independent from the main form. For an introduction see two short tutorials (overview), (tables and columns). To open a spreadsheet, choose Grid - Spreadsheets - and then one of the provided versions, e.g. Organisms from the menu. A window as shown below will open where the data are marked and organized according to the database tables. If values in one of the tables are missing, this will be indicated with a grey background. The colors correspond to the overview for the database.

Start

To use any of the spreadsheets as a starting window, click on the  button. Now the application will directly open the spreadsheet with the same parameters when you close it. 

Database

To change to another database, click on the button and choose the database as described here. Please keep in mind that the main form will connect to the new selected database. 

Project

If a user has read only projects available, a button will appear in front of the project. Click on this button to change to the list of projects with read only access. The window will change into the Read only mode (see below). To return to the list of projects with write access, just click no the button again. After changing the source for the project list, the project label will blink with red to remind you, to select a project from the list. 

Getting the data

The data are always restricted to one project, selected in the corresponding field (see image above) and restricted to the first top lines as specified in the Max. res. field. To change to the next or previous block of data, use the resp. button. 

The program will organize the data in blocks indicated by the colors as shown above. In the example above the first block contains 2  Organisms all belonging to the block starting with  Hildesheim... for the Event and M-0014196 for the Specimen. The next block then starts with  Hildesheim... indicated by a change in the color containing 2 Organisms. For most of the spreadsheets, the presence of the Event in the data is a prerequisit. As long as you do not sort or filter the data (see below), these blocks will be consistent with the data. As soon as you filter or sort the data, these blocks may be split and may not correspond to the data blocks in the database any more. In the example below you see the effect of sorting by the column Taxon on breaking up the blocks. E.g. the block for the specimen M-0036950 is split into 2.

SQL

The query used for the retrieval of the data can be accessed with a click on the SQL button.

Filtering

To filter the content of a table you can apply a filter either on the whole table or on each of the columns of the table.

Table filter

This filter will apply on the whole table. Click in the black box next to the filter area and select one of the filter options as shown below.

• ♦: Filled (all visible columns)
• ◊: Empty (all visible columns)
• •: Data in table do exist
• Ø: Data in table do not exist

Tutorial:

Column filter

Tutorial:

This filter will apply on a single column of a table. To set a filter click in the field underneath the column name. A window as shown below will open. With a click on the button you can enter a value from the current content of the column as filter.

Here you set the sorting (see below), enter the search string and choose among several ways of comparison with the contents in the database:

• =: The content must be exactly like the given value
• ≠: The content must be different to the given value
• ~: The content must be similar to the given value, use wildcards % for any string or _ for a single character
• ¬: The content must NOT be similar to the given value, use wildcards % for any string or _ for a single character
• <: The content must be smaller than the given value
• >: The content must be bigger than the given value
• |: The content must be in a given list of values
• ∉: The content must NOT be in a given list of values

For columns linked to modules of the DiversityWorkbench there may be additional options. E.g. for a column linked to DiversityTaxonNames you get 3 additional options:

• +H: Include lower Hierarchy
• +S: Include Synonyms
• +H+S: Include lower Hierarchy and Synonyms

After selecting one of these options, you will be asked for the database and the project where the data should be taken from. In the next step the corresponding names as retrieved from the selected source will be listed (see below). To change the filter click on the button and on the button to remove it.

Sorting

↓↑ Tutorial:

The data can be sorted by each visible column. If you click into the field underneath the column name a window will open as described above. To change between the modes of sorting, just click on the current sorting. The modes are:

• -: Not sorted
• ↑: Sorted in ascending sequence
• ↓: Sorted in descending sequence

After all parameters are set, the sort mode and filter settings will be shown in the field underneath the column name (see image below). The number indicates the sequence within the sorting columns.

Timeout

After all parameters are set, click on the button. If for any reason you get a timeout, meaning the query for the data takes too long, either simplify your query or adapt the time for the query after a click on the button. If you do not want to restrict the time for the queries, set the value to 0. The default value is 30 seconds. 

Read only mode

<> Tutorial:

The formatting of the sheet including the color indication of tables and data blocks is rather time consuming. If these are not needed, e.g. for exporting the data, you can switch to the Read only mode for higher performance. For projects with read only access (see above), the mode is automatically set to Read only. 

Editing

To edit the data, just change them. If data are missing, type or select a value in the corresponding field. To remove data, click on the x field. This will remove all entries dependent on this entry that means all data right from the entry in the same line resp. block and any depending data. If there are any depending data, a window will open as shown below listing these data. Click OK if you want to remove the selected data including all depending data as shown in the window.

To change the content of several values in a column, either select the whole column with a click on the  button or select the fields manually. To avoid the pop-up of data-entry windows e.g. for columns with a lookup list, click no the button. Once you have selected the contents to change, select the mode of change:

• Prepend: Insert the given value at the beginning of the content
• Append: Append the given value at the end of the content
• Overwrite: Remove current content and insert given value
• 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.

With the context menu (mark area and right click) you can Remove data (for single data fields with a list behind), Tranfer or Copy the content into the clipboard and Insert the content of the clipboard into the selected cells. Tutorial:

Locked columns

Columns that can not be edited are indicated with a lighter background color of the header and a gray text of title and content. These columns contain e.g. database generated content or data from lookup tables.

Inclusion of RowGUID

By default the primary key can not be changed in the spreadsheet. In some cases you may want to change parts of the primary key. To do this, you must include the column RowGUID in the list of selected columns. The program will ensure that the changed data do not collide with existing data, that is having the same primary key. See an example in a short tutorial:

Fixed sources

Tutorial:

For columns that are linked to a remote module, you can fix the source for the query. If the source is fixed, the query will directly contact the source as shown in the image below. To set resp. change the source, click on the button. A window will open where you can select either a webservice or a source database together with a project within the database. To remove the source, click on the button (only visible if a source is present).

To see an overview for the fixed sources, click on the button. A window will open where all sources are listed with the source for the current column marked with a yellow background. 

A "right-click" on the button in the main form will show the settings as well and with a click on the button you can set the connection for the selected column. If a column depends on values from the data as for example the relations to the module DiversityTaxonNames with a dependence on the taxonomic group, the relation will change with the selected row, depending on the data retrieved from the selected row. If there is no connection to the related module defined, the button will appear gray and if the column has no relation to a module, the button will appear like

If the source is not fixed the query will start as described here.

Settings

- To change the data shown in the query results, either click on the header of the tables, e.g. Event for that table. A window as shown below will open where you can select or deselect columns, change their headers etc. Red columns need to be filled (either by the database, the program or the user). In the Alias field you can rename the columns to your preferences. The button will show a description of the columns. For columns linked to a module, the current settings for the link will be shown in addition to the description. To display a column in the sheet use the checkbox . If a column is needed, but should be hidden, select the checkbox. Displayed columns are indicated by a yellow background while hidden columns get a light yellow background. Certain columns are required (indicated by a purple color) and can not be removed e.g. if they are involved in a link to a remote module like in the example below the columns FamilyCache and OrderCache. Columns linked to a module are indicated by a blue color.

The button allows you to include one of the tables missing in the sheet (see image below). After selection of the table, select the column(s) you want to include in the sheet as shown in the image above.

To store resp. load settings, use the resp. button. If a setting file has been corrupted click on the button to remove it and restart with factory settings. The spreadsheet will always start with the previous settings. The location where the settings are stored are set under Administration - Resources directory ... . For an introduction see a short tutorial .

Column width

Tutorial:

The width of the columns can be set manually (in the filter area) or automatically with a click on the button. A window will open where you can choose and set the parameters for setting the column width.

Adding

Tutorial:

To add new data, use the area underneath the data table. You can enter preset values that will be used for the new data. If the new data should be added to existing entries, select the corresponding row. Then click on the + field of the datarange that should be inserted. If preset values are given, all corresponding tables will be filled together with the new inserted data. Defaults for the responsibles can be set under Administration - Customize Display. If a column is linked to a remote module, the corresponding columns will be filled together with the selection of the link, so e.g. if you select a link for a taxonomic name to a DiversityTaxonNames the columns for the taxon and if available the familiy etc. will be filled as well. To remove a linked value, select it a choose Remove from the context menu (right click).

Export

Tutorial:

To export the data as a tab separated text file (UTF8), click on the button. You will be asked if you want to include the hidden columns. These are the primary keys you may need for statistic evaluations etc.

Feedback

To send a feedback to the developer of the software, create a screenshot and click on the  button. 

Details

Tutorial:

To see all details of a dataset, select the dataset in the sheet and click on the button. A window, corresponding to the main form will open, showing all data related to the selected specimen. 

Image

Tutorial:

If an image is present a preview will be shown in the right upper area of the window. Click on it to see the image in a separate form. The images are restricted to the first image of one source, so e.g. in the organisms sheet only the first image of the specimen linked with this organism will be shown while images of e.g. linked to none or another organism or the collection event will not be addressed. 

Diversity Collection

Collection Event Series

If you need a hierarchical order of your CollectionEvents or want to organize several CollectionEvents, for example, to document expeditions, you can achieve this with a CollectionEventSeries.

For a better differentiation between events and CollectionEventSeries, there is blue text in the hierarchy as well as the editing part, and a different icon . A CollectionEventSeries can contain other CollectionEventSeries and CollectionEvents. Information about the geographic locality, properties of the collection site, date of collecting etc., is stored in the CollectionEvent. To show or hide the CollectionEventSeries, you have two options. In the panel on the left of the tree the button will show the superior EventSeries of the current CollectionEvent as shown below.

The button will show the entire hierarchy of the EventSeries as shown below.

To edit the data of an EventSeries, select it in the tree to display the detail fields as shown below.

New Event Series

To insert a new CollectionEventSeries click on the button. If there are no CollectionEventSeries so far, the CollectionEvent will be placed within the new CollectionEventSeries. If there are CollectionEventSeries present, the new CollectionEventSeries will be placed below the selected CollectionEventSeries. To assign a CollectionEvent to an existing CollectionEventSeries already available in the database, click on the button.

To move an item within the hierarchy, just drag it with the mouse to whatever position it should be placed in. Keep in mind that specimens can only be placed in CollectionEvents and CollectionEvents only in CollectionEventSeries.

Removing EventSeries

If you want to delete a CollectionEventSeries or a CollectionEvent, remove all depending CollectionEventSeries, CollectionEvents and specimens and click on the  button. A specimen can not be deleted here.

If you want to remove a CollectionEvent from the current CollectionEventSeries, click on the button.

Moving into Event Series

If you want to transfer the data selected in the query results into a CollectionEventSeries, choose Data - Transfer - to event series… from the menu. If only a part of the items in the query results is selected, you will be asked whether all data in the list should be transferred. To transfer only the selected data, click NO. To transfer the entire list, click YES. Note: Only samples that are already part of a collection event can be transferred. Items without a collection event will not be included.

Images

To display the images, choose  Series images   in the header menu. To add images to a CollectionEventSeries, click the button. To remove an image, use the button. With the button you can switch to a new Chromium-based browser for the display of images. The presence of images in an event series is indicated by a yellow background on the lower of the buttons in the upper right corner. These buttons may be used as a shortcut to display the images .

To zoom a sector of the image, simply move the mouse over the image. A red square will indicate the zoomed area. To set the size of the image to the original resolution, click on the button. To adapt the size of the image to the available space in the form, click on the button. To change the orientation of the image use the appropriate buttons ( flip horizontally, flip vertically, rotate right, rotate left). To view the image in a separate form, click on the button. If the image should not be published, e.g., on the internet, enter any reason in the Withhold reason field. Besides images, you can also store other media. 

Descriptors

To add descriptors to an event series, you must first add descriptor types. Choose Administration - Enumerations - Event series - Desprictor from the menu, or click the button in the descriptor section. A window will open where you can manage the available descriptor types. Use the resp. buttons to add or remove a descriptor to the event series.

Hierarchy

If you want to change to another specimen listed in the CollectionEventSeries, select it in the hierarchy and click on the  button.

The current specimen, together with the event and all superior CollectionEventSeries will be highlighted.

Geography

The CollectionEventSeries can contain a geographical object (using WGS84) such as a point, a line, an area, etc. To edit or show the geographical object related to the CollectionEventSeries, either click on the Geography button in the details next to the notes field select the Map in the header to show the maps and use the GIS editor .

Storage

The data of the CollectionEventSeries is stored in the table CollectionEventSeries.

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Event Images

The specimens stored in a collection are gathered during a CollectionEvent. To insert an image related to a CollectionEvent, select the event image in the header menu to display the images of the collection event. In case the event images are not displayed, a yellow (image(s) present) resp. gray (no image) backgroud of the tiny buttons at the upper right corner indicates the presence of images .

In the list (see below) click on the  button. If you want to delete an image, click on the  button.  For more details see the section Images.

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

If for any reason an image should not be published i.e. shown on a website, enter the reason in the field Withholding reason. Only images where this field is empty will be shown e.g. on websites. The EXIF data are extracted from the image during the import, e.g. via DiversityMobile.

Data is stored in the table CollectionEventImage .

Diversity Collection

Geography

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

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

The data of the geography of the taxa are stored in DiversityTaxonNames in table TaxonGeography.

Diversity Collection

Maps of samples in the database

If there are WGS84 coordinates available for your collection site, an event series or single organisms, you can use GoogleMaps to display these locations.

To use this service you need access to the internet. Select the Map for display in the header area to show the maps. Here you can display maps of CollectionEventSeries, CollectionEvent, Organism as well as Distribution maps. To display the maps you can either use the browser, the web viewer, the GIS viewer or the GIS editor. By default the map will show the location of the CollectionEvent using the browser as shown below.

The two options browser and web viewer in principle provide the same function, but rely on different controls. Due to incompatiblities between controls and the google web API you may have to test both to display a map.

For the CollectionEventSeries, the CollectionEvent or the Organism you can use any geographical object like points, lines, areas, etc. to describe the location. The browser will always display these objects as points (see left image below) whereas with the GIS editor you can see and edit the real objects (see right image below).

The data of the geographical objects is stored in the table CollectionEventSeries for the collection event series, the table CollectionEventLocalisation for the collection event and the table IdentificationUnitGeoAnalysis for the organisms.

Diversity Collection

Distribution maps

If WGS84 coordinates are available for your collection sites, you can create distribution maps of your samples in the database. To use this service you need access to the internet. Choose Map in the header to show the maps. To display distribution maps choose the appropriate option from the first drop down list in the mapscontrol.

To add data sets to the distribution search for the data sets you want to see in the map, mark them in the list (either use the button to mark all data sets, mark a list/single data sets or check the option for the distribution map) and click the button. To display the map click on the button. The displayed localities in the map will not change until you add new localities or click the button to start with a new distribution map. If you want to set different icons for the positions of different series of your samples, set the style of the icon (symbol, color, size etc.) in the menu before you add them to the distribution list.

To show a distribution map of all the specimens found in your query as shown below, select the option Distribution from the drop down menu. For the display in the map you can choose either the Browser (see below) or the GIS-Editor. In the browser all objects will be shown with their center coordinates and the number of specimens that can be depicted is limited, thus, it may be necessary to restrict your query. With the GIS editor all objects will be shown with their whole geography (e.g. an area will not be reduced to its central coordinates) and there is no limit to the number. Furthermore you can vary the symbols for different groups.

The upper distribution map is restricted to coordinates of the collection event . If you want to include coordinates from the organisms , choose the distribution map including organisms . For the positions of the organisms in this map, the ID of the organism ( = IdentificationUnitID, 528577 in example below) is shown as identifier and the last identification ( = LastIdentificationCache) as display text (Ajuga reptans L. in example below).

If you want to restrict the display to the organisms, click on the  button to open the window for custimizing the display (see below) and deselect all localisation systems for the collection event.

While in the GIS tool the objects are represented with their real geography (see above), in the browser every object is reduced to a single point. For an introduction see a short tutorial .

Diversity Collection

Sampling Plots

If your samples are collected at constant sampling plots, you may use the module DiversitySamplingPots to describe said SamplingPlots. For a better differentiation between events and the SamplingPlots there is a brown text in the hierarchy as well as a different icon . A SamplingPlot can contain other SamplingPlots and CollectionEvents. Information about the geographic locality and properties of the collection site can be stored in the SamplingPlot, while the collecting date must be stored in the CollectionEvent. To show or hide the SamplingPlots you have two options. In the panel on the left of the tree the button will show the superior SamplingPlots of the current CollectionEvent as shown below.

The button will show the entire hierarchy of the SamplingPlots as shown below.

If you select a SamplingPlot in the hierarchy, two buttons will appear in the bar to the left of the tree. With the button will show the entire hierarchy of the SamplingPlots as shown below.> button you can retrieve a taxon list for the SamplingPlot. With the button you can retrieve a summary of the information on a SamplingPlot (see image below).

To edit the data of a SamplingPlot please use the module DiversitySamplingPlots.

The link to the module DiversitySamplingPlots is stored in the table CollectionEventLocalisation.

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Habitats and properties of the collection site

For the description of the habitat select the CollectionEvent or an existing collection site property . The description is entered in the field Habitat (see below).

To enter a new property of the collection site select the CollectionEvent or an existing collection site property . Then choose the type of the property you wish to enter from the drop-down menu as shown below. Only items which are not already set for a CollectionEvent will appear in the list. You can customize the selection of visible items.

The list is dependent on the availability of terminologies for site descriptions. Details for the property can be entered if you choose the item in the hierarchy. The person responsible for the entry as well as notes can be entered in the corresponding fields as shown below.

To delete entries use the  button. You can enter a value by either typing the name of the collection site property or by selection from the module DiversityScientificTerms. To search for properties from this module click on the  button. The current user’s name will be inserted as the responsible user. You may change this by either typing or through selection from the module DiversityAgents.

As an alternative to the button, you may select the property via a chart with a click on the button. A window as shown below will open. To select an item from the chart click no the entry you want to select and close the window with a click on the OK button.

The data concerning the habitats is stored in the table CollectionEventProperty.

Administration of properties (resp. terminologies)

To administrate the available properties of collection sites, choose Administration - Site properties… from the menu. A window as shown below will open, where you can delete existing site properties and add new site properties.

To add new properties, click on the button, select the new entry in the list and choose the appropriate parsing method.

Properties should be linked to the module DiversityScientificTerms. To link the property to the module, click on the  button. A window as shown below will open, where you can search for the terminology provided by the module. Please keep in mind, that the ID of the terminology will be used for the new entry and that this ID must be unique. Turn to your administrator if any difficulties occur.

After choosing the terminology from DiversityScientificTerms, the new property will be displayed as shown below..

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. 

Diversity Collection

Organisms

(= Identification Units)

The items or organisms in one CollectionSpecimen are regarded as IdentificationUnits. One specimen can contain several IdentificationUnits e.g. an insect (1) feeding on a fungus (2) growing as a parasite on a plant (3). To add a new organism use the drop-down menu as shown below to select the taxonomic group to which the new organism belongs to.

To specify the taxonomic groups that are shown in the drop-down menu select Administration - Customize display ... from the menu.

The organisms of the specimen are shown in the tree. To edit the relations between the organisms simply drag and drop. In case of a shortcut in the hierarchy you will be asked to select the start of the hierarchy as described in the video: . The name of the organism under which the specimen is stored in the collection is [underlined]. To delete an organism select it in the tree and click on the button.

To enter details about one of the organisms like e.g. gender or life stage, select it in the tree. The fields for the details of this organism will be displayed in the right area of the window as shown below.

If the Identification unit is e.g. not a complete organism you can enter a description for this IdentificationUnit. Either type you description or choose one of the predefined descriptions via combobox or hierarchy: Use the combobox to select a description as found for the same taxonomic group in the database or use the hierarchy-selector to select a predefined description. An additional description can be entered for an IdentificationUnit within part of a CollectionSpecimen.

Taxonomic hierarchy - family and order

The entries for the family and the order of the taxon are either set when linking to a taxonomic database or set manually when no link to a taxonomic database exists.

If no link to a taxonomic database exists you may enter the family and the order after clicking on the button. To transfer these entries to other specimens with the same genus use the maintenance functions as described under Maintenance - family andorder.

Parts of units

If a unit contains parts which have to be documented, you can do this by setting the relation to the substrate to "Part of".

In the tree the background of a part will be grey as shown below for the unit-tree und the tree depicting the storage of a sample. The name of the part will correspond to the identifier set for this part. The icon will correspond to the description of the part provided you choose one of the preset options contained in the drop-down list. You may of course enter any description for the unit. A unit that is part of another unit can not get an identification. Identifications are restricted to the main unit.

Parent-child relations

If a unit is a genetic child of a parent, choose "Child of" as type of the relation. If there are 2 parents like mother and father that you want to document, click on the button next to the relation type. A window will open where you can choose among the organisms (= units) in your sample. The second parent will be indicated with the symbol in the tree (see below).

For details about exsiccatal series and analysis see the related topics. You can sort your IdentificationUnits e.g. for display on a label with the displayorder button. Each IdentificationUnit can have several identifications.

With the template you can define and copy predefined values into the data (see chapter Template).  

If there are images which are related to the current organism, the button for the restriction of the images will be enabled ( → ). Click on it to restrict the images to this organism. The button will get a red background to remind you about the restriction and in the image list a button will appear that enables you to show all images.

Non biological units

Non biological units like soil, rock or mineral do not have biology related characters like family or sex. These are therefore not displayed for these groups. 

The data for the organisms and non biological units are stored in the table IdentificationUnit.

Diversity Collection

Taxonomic Group

The organisms and corresponding objects stored in the database are organized in taxonomic groups to facilitate the recognition in multi organism samples and to enable a specific design for the analysis where e.g. plants differ in recorded measurements from mammals. The taxonomic groups are roughly orientated on the taxonomy but are not meant to replace the taxonomy for which there are other possibilities for entry. The list of taxonomic groups visible for the creation of new entries may be restricted as described in the chapter about the customization.

To administrate the taxonomic groups, choose Administration - Taxonomic groups... from the menu. A window as shown below will open. 

To add resp. remove a taxonomic group use the resp. button. To set the superior taxonomic group use the button. With the button you can set a symbol for the taxonomic group. Please keep in mind, that this will be converted into a 16 x 16 size icon. In the lower part of the window, you can add and edit translations for display texts, abbreviations etc. for all contexts available.

If a taxonomic group has been disabled it will not appear in the lists for the user and will be displayed without an image in with grey text color in the tree (see below). After reenabling a group you have to reopen the form to see the icon for the group.

At the base of the window, the projects that are restricted to an entry are listed (see ). To administrate the projects that should restrict the available taxonomic groups, choose Administration - Enumerations - Project - Taxonomic group... from the menu. A window as shown below will open. If a project is restricted, the client settings will be ignored (see chapter Customize). 

To add resp. remove a material category for a project use the resp. button.

The non-biological taxonomic groups like soil, rock or mineral will for an identification not be linked to DiversityTaxonNames but to DiversityScientificTerms (see image below and the short tutorial ). If you add a new taxonomic group anything outside the predefined groups animal, alga, bacterium, bryophyte, fungus, gall, lichen, myxomycete, plant or virus will be regarded as non-biological. The sources for direct access using the buttons are linked to the taxonomic groups (see Settings).

Diversity Collection

Retrieval Type

The ways the data about organisms and corresponding objects stored in the database are retrieved are documented as retrieval type.

To administrate the retrieval types, choose Administration - Retrieval types... from the menu. A window as shown below will open. 

To add resp. remove a retrieval type use the resp. button. To set the superior type use the button. 

Diversity Collection

Analysis

The organisms in a specimen can be analysed by analysis types defined in the database. In the tree the analysis entries are symbolized with an icon. Only the types of analysis that were assigned to the group of the organism can be selected. An analysis always refers to an organism and may also refer to a part of a specimen. An analysis that refers to a part of a specimen will be shown in the tree for the parts as shown in the examples below.

To show or hide the analysis items in the tree use the button in the left panel. This button has 3 states. In the default state the analysis entries will be shown as above. If you click a second time it will change to the hierarchy mode and the entries will appear as shown in the tree below. The last state will hide the entries.

To insert a new analysis to an organism select the organism in the upper tree. Then select the type of the analysis from the drop down list as shown below.

To delete an analysis, select it in the tree and use the button in the panel on the left. To edit the details of an analysis, select it in the tree and enter data into the fields as shown below. To enter or inspect an URI given for a single analysis, click on the button.

If an analysis refers to a part of the specimen, you can document this by choosing the respective part from the list (see field Part above). The analysis will then be shown in the tree for the parts of the specimen as well. Alternatively you may directly choose the organism in the part tree and create the analysis for this part of the organism in the part tree. If you used any tools defined in the toolsection, you can include the usage of these tools.

In case the measurement unit of the analysis set to DNA (see below) ... 

... the Result is edited as shown below.

A click on the button opens a separate window (see below) with additional options for editing the sequence.

Administration

If you require further information about an analysis click on the button. A window for the analysis administration will open. If you have the proper rights you can edit the analysis types used in your collection as shown below. This window is also accessible via the menu entry Administration - Analysis...

For the import and export of data it is sometimes necessary to know the IDs of the analysis types. To see the IDs, click on the [ ID] button to display them as shown in the image below.

The types of an analysis are restricted by the taxonomic group of the organism or object to be analysed and from the projects. You may edit the list of taxonomic groups resp. projects, which can use a certain analysis, using the and button. To add all used taxonomic groups resp. projects, you can use the buttons. For details about handling data see the data section. If you add a taxonomic group or a project to an analysis, all children of this analysis will be available for these taxonomic groups resp. projects as well (see image below). Thus, in the example above it is sufficient to enter the taxonomic group and the project in the analysis Mammals to have access to all analysis within this superior analysis as shown in the tree. The different types of analysis are organized in a hierarchy. To organize. Some of the entries may only serve for structuring purposes (e.g. Mammals as shown above) and should not be used to document the analysis of the specimen. To ensure this, check the checkbox [Only hierarchy]. 

There are 3 states for result lists in the main form. (1) No result list will be generated if a measurement unit is defined, for example if you specify "mm" as the measurement unit. (2) If no measurement unit is defined, the program will collect all values given so far and present these values as a list. (3) Some types of analysis need categorized values. Enter these values together with their description in the Result list as shown below using the and buttons respectively. To show values different from the entries in the Result column change the entries in the Display text column.

If you want to access or inspect an URI given for an analysis type, click on the button. The URI related to the analysis will then be displayed in the window below.

Besides of a plain text description of the analysis, you may insert methods as defined in the chapter Methods. Use the and buttons to add or remove methods from the list (see below). The added methods will be marked with sequential number (see Mark.: ... ) to allow several methods of the same type.

Every method may have several parameters that will automatically be available to take your values. If the definitions of the parameters have been changed, you may add missing parameters with the button. A window as shown below will open where you can select the missing parameters you want to add.

To view the history of a dataset, click on the button. A window with the history will open. For more details see the section History.

Diversity Collection

Geography of organisms

The geographical position of organisms (using WGS84) can be recorded along with the date, for example, to document migration patterns or the distribution of an organism. In the tree, the geographical entries are symbolised by an icon, as shown below.

To display the corresponding map, activate Maps and click the button. To edit an existing geographical entry, use the GIS editor. If you are adding a new geographical position and existing entries are already shown on the map, remove them from the map before inserting the new location.

Diversity Collection

Identification

Each organism or unit may have been identified several times. The identifications are listed in the tree under the organism as shown in the image below. To create a new identification choose the organism from the tree and click on the icon. The last identification will always be taken as the valid one and set at the top of the list. To insert an older identification at the base of the list click on the icon.

To hide / show the identifications in the tree click on the icon on the right panel next to the tree. To enter a confirmation of an identification choose it in the tree and then click on the button. To move an identification to the end or the start of the list use the or button respectively. To delete an identification select it in the tree and click the  button. To enter details for an identification choose it in the tree. You can then enter the details in the form opening on the right side of the tree as shown below.

The taxonomic name of an organism can be selected from either the names already available in DiversityCollection or from the module DiversityTaxonNames. To choose from the local names type the beginning of the name and click on the drop-down button  to get a list of available names. You can use wildcards according to SQL.

To select a taxonomic name from an external database click on the button. A window will open where you can search for a taxonomic name. For taxonomic names provided by the module DiversityTaxonNames you can use a shortcut. Click on the button to set the source in the window that will open. After the source is set, the pin and drop-down box will change their colors as shown below to indicate that the taxonomic names are not longer derived from the content in DiversityCollection but from the selected DiversityTaxonNames database.

The links will be set separate for every taxonomic group and may be changed at any time with a click on the button. To release the link to the remote database, click on the  button and than select Cancel in the window where you select the database. The pin will change to and the data will again be derived from the local values in DiversityCollection.

For identifications linked to a DiversityTaxonNames database you may activate the Show accepted names option. Accepted names will then be shown with a green color while for synonyms the accepted name will be displayed above the current name (see below).

Non biological units

Non biological units like soil, rock or mineral do not have biology related information like a qualifier or a type status. These are therefore not displayed for these groups. Furthermore the source for the names is not DiversityTaxonNames but DiversityScientificTerms (see a short tutorial , ). If the source for a non biological unit is set to a DiversityScientificTerms database (see above ) a button will appear. With a click on this button you can select the term from a chart as shown below.

In the database the data for the identification is stored in the table Identification.

Diversity Collection

Supplementary (dependent) identification

For an identification of a non biological unit with the source DiveristyScientificTerms you may add a supplementary identification . The availability of this option depends on the first identification. For example a geological sample with the identification "Basanit" may get supplementary identifications like "Glasige Matrix" of the type "Zement/Matrix" and "Porphyrisch" of the type "Relative Korngrösse". The available supplementary types are defined in the module DiversityScientificTerms. For further information about dependencies among terms please consult the manual of DiversityScientificTerms.

To insert a supplementary identification related to DiversityScientificTerms click on the button. A window as shown below will open with the database set according to the main identification and the available term restricted to those as defined as dependent to the selected type of the main identification as defined in the DiversityScientificTerms database.

The type of the supplemental name is included in front of the supplementary name as shown below and a type can be given several times to indicate ranges or distinct items.

Diversity Collection

Taxon List

Tutorial:

To see the list of organisms within a Specimen , CollectionEvent , EventSeries or SamplingPlot click on the button which will appear, if you select one of the corresponding items in the tree (see below).

A window will open as shown below where you can gather additional information stored in the module DiversityTaxonNames. You may include the sex and the sum of the number of units as stored in table IdenticationUnit or the number based on the organisms in the list.

To retrieve information stored in the module DiversityTaxonNames for names which are linked to this module select the taxonomic group of the organism. Then select the option Include information from taxonomic lists. A combobox will appear where you may select the taxonomic database. Next, select the project in the combobox and finally the analysis. After all options are selected, click the button to refresh the data. With the From and Until option you can restrict the result depending on the collection date. To export the results in a tab-separated list use the button.

Diversity Collection

Part

Parts of the specimen

A specimen can contain several parts which may be stored in several collections. These parts may represent different material categories, e.g. herbarium sheets, microscopic slides etc. The parts are shown in the part tree under the main tree. This tree depicts the parts either in accordance to their relation to each other in the specimen tree (click on the icon in the panel on the left) - see first image below - or in relation to the collections where the parts are stored (click on the icon in the panel on the left) - see second image below. Here the two parts of the specimen are located in two collections. To add a new part use the drop-down field in the panel on the right of the tree and choose the material category of the new part. The material categories which appear in this list can be customized. You can set the a default collection for new parts. If the default collection is not set, you will be asked to name the collection of the new part. If the part is derived from another part, select this in the tree before creating the new part. The new part will then be added as a child of the old part. You can later edit these relations by drag & drop. If you wish to create a copy of a part, use the button in the panel on the right side of the tree. To insert parts when the tree is hidden use the button and follow the upcoming dialogs. As another option you can transfer all specimens in the result list of a query via the menu Data - Transfer - To collection ... into a collection. Please keep in mind that next to adding part existing part will be transferred to the selected collection as well.

To see the whole content of a collection, click on the button. All specimens within the collections will be listed as shown below with e.g. their accession number, accession number of the part, storage location, collection date and/or locality as set in Customize . 

If an organism is present in a part of the specimen, it will be shown in the tree. To edit its presence select the specimen part in the tree and edit the Display order as shown below.

In the example above, all organisms are present in the specimen. However, the fungus Cystotheca lanestris was chosen not to appear on the label and was transferred to the Hide list. This is symbolized by a grey icon in the tree. You may enter a description for an organism as a whole or for the organism within a certain part. The slide, symbolized by the icon, was created from the sample. Thus, in the specimen tree it is shown as a child of the specimen symbolized by the icon. Concerning the organisms only the fungus Arthrocladiella is found on the slide. Thus, in the tree it is the only organism shown as child of the slide. In the display order the two other organisms appear in the Units not in part list (see below).

To move the organisms between the lists use the > and < buttons. In the list Show in label you may change the sequence of the organisms with the and buttons in the panel at the base of the list. The organism at the top will be the one taken as the main organism, e.g. for printing a label.

To see changes of the stock of the part click on the button . A window will open listing all previous volumns together unit, the date and the responsible user.

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).

To edit the details of a part select it in the tree to open the fields as shown below.

The identifier, e.g. the taxonomic name under which the specimen can be found in the collection is entered in the field Storage location. You can search for this entry in the query.

With the template you can define and copy predefined values into the data (see chapter Template).  

To search for a free accession number use the button (see chapter Accession). To enter the storage location you may use the drop-down button to select from e.g. the identifications within the specimen. The source for the list can be specified under Administration - Customize display ... (see below). 

The drop-down button for the Notes will provide you with a list of all entries in this field, filtered with your entry in the text field. You may use wildcards like "%" or "_" (see Wildcards).

In the collection tree, the specimens are shown with their dependence upon each other based on their location in Collections. To get information about a collection simply select it in the tree. If you have the required rights, you may use the button to open the administration of the collections. This form is accessible under the menu entry Administration - Collections... as well.

The material category of a specimen part is indicated by the icon in the hierarchy.

Here some examples:

bones: bones or skeleton from vertebrates
cultures: living cultures of organisms
drawing: original line or color drawing
herbarium sheets: capsules or sheets as stored in a botanical collection
icons: icons, images etc. stored in a botanical collection
micr. slide: glass plate with sections of specimen for microscopic studies
specimen: specimen stored in a collection\

Specimens can be included in a transaction. Every stored part of a specimen may be treated with several processings.

If there are images which are related to the current part, the button for the restriction of the images will be enabled ( → ). Click on it to restrict the images to this part. The button will receive a red background    to remind you of the restriction and in the image list a button will appear which enables you to show all images.

To edit the parts of the specimens in a table see the chapter Grid forparts, use the Table editor for the Part table or the Part sheet from the Spreadsheets.

The data is stored in the table CollectionSpecimenPart.

Diversity Collection

Parts

Material categories

The objects stored in a collection is organized in material categories to facilitate the recognition of specimen containing diverse materials and to enable a specific design for the processing where e.g. bones differ in treatment from DNA samples. The list of material categories visible for the creation of new entries may be restricted as described in the chapter about the customization.

To administrate the material categories, choose Administration - Material categories... from the menu. A window as shown below will open. 

To add resp. remove a material category use the resp. button. To set the superior material category use the button. With the button you can set a symbol for the material category. Please keep in mind, that this will be converted into a 16 x 16 size icon with black regarded as background and translated to transparent . For the translations for display texts, abbreviations etc. please see the chapter about database description.

At the base of the window, the projects that are restricted to an entry are listed (see ). To administrate the projects that should restrict the available material category choose Administration - Enumerations - Project - Material category... from the menu. A window as shown below will open.  If a project is restricted, the client settings will be ignored (see chapter Customize).

To add resp. remove a material category for a project use the resp. button.

To add a more detailed description of a part, please use the Descriptions of specimen parts and are involved in the mapping for ABCD.

Diversity Collection

Processing

Every specimen can be processed, e.g. for preparation or preservation. Processings can be applied to a specimen or a part of a specimen. In the hierarchy for the parts the processings are indicated by the icon and a blue text. If there are any processings available, they will be indicated by the icon in the tool bar. Please keep in mind that the availability of the processings depend upon the material category and the current project as described below. You can hide or show the processings in the hierarchy with a click on the icon in the very left bar (see below). The images below show a processing in the collection and the specimen tree for the parts respectively.

You can enter a new processing for either the entire specimen or a part of the specimen. To do this select the specimen or part in the hierarchy and choose a processing from the list as shown below.

The duration of the processing is saved in ISO8601 format by default indicated by the ISO icon with separate fields for year to second (see below). To change to text format, click on the ISO icon that will change to ISO and the separate fields will be replaced by a text box containing the value. If separate fields are only available if the value is in ISO 8601 format. If the start date for the processing is given the processing duration can be set via the calender. In case of the ISO format selected this will be translated into the corresponding period. In case of the ISO format deselected the date will be inserted. See a short introduction for an overview:

To delete a processing select it and click on the button. To edit the data for a processing select it in the hierarchy. The window will show you the fields related to the processing. You may add methods for the processing as defined in section Method. 

(If you previously used any tools defined in the toolsection, these are deprecated and replaced by methods).

Administration

If you have the required rights you may edit the processing types in the menu entry Administration - Processing...

In this window you can define the processings used in your collection. To add a new processing click on the button, to delete a processing select it and click on the button. The processings are related to material categories within the database. To add a new material category or projects, which should be connected to the selected processing, click on the button in the panel right of the material categories or the projects. A window will open where you need to select the desired material category or project respectively (see below).

The processing types are organized in a hierarchy. Some of the entries may only serve for structuring as Maceration in the example below and should not be used to document the processing of specimen parts. To ensure this check the checkbox [Only hierarchy]. For the import and export of data it is sometimes necessary to know the ID's of the analysis types. To see the ID's of the data sets click on the [ID] button. The ID's will then be displayed as in the image shown below.

Besides of a plain text description of the processing, you may insert methods as defined in the chapter Methods. Use the and buttons to add or remove methods from the list (see below). The added methods will be marked with sequential number to allow several methods of the same type. Every method may have several parameters that will automatically be available to take your values. If the definitions of the parameters have been changed, you may add missing parameters with the button. A window will open where you can select the missing parameters you want to add.

To view the history of a data set, click on the button. A window with the history will open. For more details see the section History.

The data of the processing is stored in the table CollectionSpecimenProcessing.

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Description of the parts of the specimen

Tutorial:

A part of a specimen may be characterized with links to a standardized vocabulary from DiversityScientificTerms. Use the button to add and the button to delete descriptions (see below). If the description refers to a certain unit, you may select it in the list as shown below. 

The data is stored in the table CollectionSpecimenPartDescription

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Image Description / EXIF

The EXIF content is derived from the original image (see below). This will be automatically extracted from the image.

To extract the EXIF content of an image, the image must be accessible from a local directory and the exiftool.exe (see below) must be available in the application directory.

Diversity Collection

Media

Next to images you can store audio and video files. Click on the [>>>] button (see below)

To open Windows Media Player and play the content of the media. You must have Windows Media Player installed to use this function. For the description of a medium see the chapter Image description.

Diversity Collection

Media Service

The webservice DiversityMediaService provides the possibility to upload media files like images, audio recordings, etc. to a server. The usage of this webservice includes several preconditions (please turn to your administrator):

• You need an account in the DiversityWorkbench module DiversityAgents with your login in DiversityCollection linked to this account
• Your project has to be registered on the server
• You have to rename your media file according to the settings of the server e.g. using a GUID (see image below)

Use the upload button to upload your image to the server.

Diversity Collection

Collection

The parts of a specimen can be stored in several collections. To see the place where a specimen or parts of it are stored use the lower tree and click on the icon to select the display according to the collections as shown below and in a short tutorial .

In the tree shown above select the collection to display the data fields as shown below.

To be able to edit the details of a collection, you must be a collection manager of this collection. The restrictions for the access for editing the collections are defined in the CollectionManager section.

At the base of the fields you find the default collection, used for the creation of new specimen parts. Specimen parts that are not created as a part of another part will be placed in this collection. Use the button to edit this entry (see below) For another possiblity to edit this value choose Administration - Customizedisplay from the menu.

Administration of the collections

If you need further information about a collection click on the button or choose Administration - Collections... from the menu to open the window for the collection administration (this menu entry is only available for collection managers). This will open a window (see below) where you can edit the collections used in your database for which you are a collection manager. You can choose among several options to show resp. hide the hierarchy:

• Show whole hierarchy
• Superior datasets and children of current dataset
• Restrict to superior datasets
• Hide the hierarchy

Cache tables for the hierarchy

To improve the responsiveness of the application the hierarchies of the collection are cached in tables for the collection, the location and the user availability. These cached data must be kept in sync with the main data.

After changes in the collections or their hierarchy a button will remind you to save the changes in the cache tables. The list below contains all objects in the database involved in the caching of the data

CollectionHierarchy

• Accessed by user
  • view CollectionHierarchy_All
  • table function CollectionHierarchyAll based on CollectionHierarchy_All
• Behind the scenes to provide cached data
  • stored procedure procRefreshCollectionHierarchyCache
  • table CollectionHierarchyCache
  • scalar function CollectionHierarchyRefillBlocked
  • table function CollectionHierarchyRefillCache
  • table function CollectionChildNodes

CollectionLocation

• Accessed by user
  • view CollectionLocation_All
  • table function CollectionLocationAll based on CollectionLocation_All
• Behind the scenes to provide cached data
  • stored procedure procRefreshCollectionLocationCache
  • table CollectionLocationCache
  • scalar function CollectionLocationRefillBlocked
  • table function CollectionLocationRefillCache
  • table function CollectionLocationChildNodes

UserCollectionList

• Accessed by user
  • view CollectionListForUser
  • table function CollectionLocationAll based on CollectionListForUser
• Behind the scenes to provide cached data
  • stored procedure procRefreshUserCollectionListCache
  • table UserCollectionListCache
  • scalar function UserCollectionListCacheRefillBlocked
  • table function CollectionChildNodes
  • table CollectionUser_log + trigger for logging of delete

ManagerCollectionList

• Accessed by user
  • view CollectionListForManager
  • table function ManagerCollectionList based on CollectionListForManager
• Behind the scenes to provide cached data
  • stored procedure procRefreshUserCollectionListCache
  • table UserCollectionListCache
  • scalar function UserCollectionListCacheRefillBlocked
  • table function CollectionChildNodes
  • table CollectionManager_log + trigger for logging of delete

Specimen placed in the collections

With the botton, you can display the specimen stored in a collection within the hierarchy (see below).

As an alternative the specimens stored in a selected collection can be listed in the specimen list. You can hide / show this list using the [  ]/ button. The specimen list will appear as shown below. Click on the collection in the tree view to fill the list and see the specimens that contain parts which are placed in the current collection. To transfer the parts of certain specimen from the current collection to another collection, choose them in the list and click on the button. To change to a specimen from this list click on the button.

As an alternative you may select the specimen in the main form a choose Data - Transfer - To Collection ... from the menu. A window will open where you can select the collection in which you want to transfer the specimen. With this option [ALL] parts of the selected specimen will be transferred into the selected collection.

Creating new collections

To create a new collection use the button either above the Query results or the button right of the hierarchy, where the new collection will be placed underneath the collection selected in the hierarchy. To copy a collection either use the button or the button. The latter will copy the collection including all child collections. To set the superior collection, use the button. The user creating the new collection will automatically be inserted as a collectionmanager for this collection. To remove a collection, any collection manager must be removed from this collection first. Click on the button to open a window for the administration of the collection managers. For new versions of the database the removal of the link of collection managers to deleted collection will be done automatically. To transfer collections in the list as children into another collection, click on the button in the upper left corner.

Administration of collection types

To administrate the types for the collections, click on the button. A window will open where you can create new types and add icons representing a type (see below).

Use the     buttons to add resp. remove a type and the     buttons to handle the hierarchy. For new types you can use the button to add an icon for the new type.

The type regulation is provided for the collections that are meant to administrate the access to transactions of the type regulation. See chapter Transaction or further details.

Images

If there are images depicting the collection a yellow background will indicate the availability of these images. To show the images, click on the show images button. The button will get a red background and this will open the area for the images as shown below. Use the new and delete buttons to add or delete images of your collection. For further details about handling images see chapter Images.

Plan

If a floor plan is available for a collection this will be indicated by a yellow background . For details see chapter collection floor pan. 

Label

To print labels for e.g. drawers, click on the print button. The area for printing the labels will be shown (see below). Further details about printing labels are described in the chapter Label.

For the generation of QR-Codes there are 2 options:

• Collection name: The name of the collection will be coded in the QR code.
• Stable identifier: Provided the stable identifier for the database is set, the ID (= CollectionID) will be coded in the QR code e.g. http://development.diversityworkbench.de/collection_Test_2/Collection/55.

Data in tables

To edit the contents of the tables in the table editor select   - Collection resp.   - Image  from the menu. For Details see chapter TableEditors.

History

To view the history of a dataset, click on the button. A window with the history will open. For more details see chapter History.

Data

For details about handling data see the Data section. Data of the collections is stored in the table Collection.

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Collection Manager

Collection managers are users with the right to edit the transactions for a collection, including loan, purchase, inventory etc. To administrate the collection managers you must be in the administrator group. Either choose - Administration - Transaction management - Collection managers from the menu or Administration - Collection and there the button to open the editing window for the collection managers as shown below.

Use the < and > buttons to edit the list of the collections for which the selected collection manager can create and edit transactions.

After changes in the collection managers you will be reminded to save the changes in the cache tables.

The collection managers can be listed with their names or their logins. Change this with the list by option at the base of the list. If after e.g. a database have been moved to another server, the may exist logins with names not matching those on the server. Click on the agent synchonisation button to correct this. In case of duplicate permissions you might get a list with these duplicates where you have to remove the duplicate permissions.

For details about handling the collections see the Transaction section. Data of the collection managers is stored in the table CollectionManager.

Diversity Collection

Collection User

The access of users to collections can be restricted. To edit the collection list for a user choose - Administration - Transaction management - Collection users ... from the menu. A window will open, where you can add or remove collections a user has access to as shown below. The access [includes all subordinate collections]. This means adding a collection to the list a user has access to also grants the user access to the subcollections as defined in the hierarchy of the collection. In the example shown below the second entry is not necessary as it is already included in the first entry.

Use the < and > buttons to edit the list of the collections for which the selected user has access to.

After changes in the collection users you will be reminded to save the changes in the cache tables.

If a user has no collections in the list, all collections are available for this user.

A collection manager has access to the collections he is allowed to manage as well as those in the list as a collection user.

Data of the collections is stored in the table CollectionUser.

Diversity Collection

Collection Location

Tutorial:

There are 2 hierarchy available for collections (showing the whole hierarchy or only the parent datasets):

• Administration
• Location

To enable the location hierarchy, either in the custom settings - in the menu choose  Administration - Customize display...  and then in the Defaults and miscellaneous tab set the option or in the collection window click on the in the top.

By default the hierarchy according to the administration is displayed (see example below).

The location nodes in the tree indicate that these nodes have a location parent, different from the administration parent. To change to the hierarchy according to the location select the  option underneath the hierarchy (see below).

To set resp. remove a parent location click on the     resp.    button. With the    button a window will open where you can choose the parent location for the current dataset.

After changes in the collections or their hierarchy a botton will remind you to save the changes in the cache tables.

As an alternative to transfer collections in the list as children into another parent location, click on the Transfer to location button in the upper left corner with a brown background, right of the Transfer to parent collection that refers to the administrative hierarchy of the collections. A Window will list all locations in the current database and the software will ensure that the transfer will not lead to loops in the hierarchy. Transfers that would result in a loop will be listed in an error message.

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Floor plan resp. geometry

If a floor plan is available for a collection this will be indicated by a yellow background. To provide the floor plan of a collection choose from the menu and click on the button to select the floor plan. Click on the button to save the plan.

To provide the geometry of a certain area within e.g. a drawer the same can be applied with an image of the drawer as plan. The floor plans are inhertited to depending collections and the geometry of a parent collection will be indicated by a dotted line (see below). The field Height keeps the height of e.g. a sensor for temperature.

Besides floor plans you may as well specify certain positions within e.g. a drawer (see below and the tutorial ).

Restriction of access to files

The access to files on the server can be restricted with a .htaccess file within the directory. An example for the content of the file is shown below

AuthType basic
AuthName "Protected Directory"
AuthUserFile /.htpasswd
AuthGroupFile /dev/null
Require valid-user

To allow users access to the directory these users must be listed in the .htpasswd file

Run the following command to create an .htpasswd file for a user (replace user1 with the desired username): htpasswd -c /.htpasswd user1

Enter a password for user1. The encrypted password will be stored in the .htpasswd file. Confirm that the .htpasswd file has permissions set to 644.

Setting the scale: ↔

To set the scale for a floor plan with a scale provided in the plan, click on the ↔ button. A blue bar will appear that can be dragged and changed in length to a object of known size, e.g. a scale in the plan. After the scale is set, click on the button and the floor plan will be overlaid with the scale as shown above. The width of the whole plan will be shown in field [Width].

Setting the geometry: □

To set the geometry of e.g. a room, click on the □ button. A red rectangle will appear as an overlay in the plan that can be dragged into the right position. The × button removes the geometry from the current dataset. Click on the button to store the geometry.

Zoom

To zoom the floor plan use the slider at the left or the mouse wheel. To return to the original size with a click on the [1:1] button. If the current dataset has a geometry you can use the [ ]  button to zoom in the geometry. With the  button you can show the whole image. 

Diversity Collection

Transaction Loan

Loans of specimen from a collecting are documented with the transaction type loan (see below).

For a loan granted to a loan taker, create a new transaction and set its type to loan. The loan needs an administrating collection, which is the collection in which the specimen included in the loan are located and for which the current user is registrated as collectionmanager . The addresses are entered as links to DiversityAgents in the From and To areas. The To area provides a recipient for inclusion in the address. The collections in the From and To area may be used optionally as source of the address. The Begin and End fields mark the time span for the loan. If the time of the loan should be prolonged, use the Prol.: field to enter the new end date. Standard comments can be edited (Admin only) in the Customize section. In the Sending, Confirmation and Reminder sections you can create documents for the communication with the loan taker. Documents as sent to or received from the loan taker are available in the Saved documents section. If after the end of the loan all or a part of the specimen are returned, create a Return transaction as child of the loan (see image above) and include all returned specimen in this return transaction.