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 delete 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.

Diversity Collection

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  new 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

Localisation

Geography

As additional information to the description of the locality you can use several localisation systems, e.g. georeferencing. These entries are marked with an icon in the tree as shown below.

To add a new entry choose the localisation system from the drop-down list as shown below. Only items which are not already set for a CollectionEvent will be shown. The items visible in the drop-down list can be customized.

If a localisation should be removed, select it from the list and click on the  button.

GIS editor

To define an area for the locality you can use the GIS editor. For further details please see the help sections for the corresponding pages.

Coordinates (WGS84)

If you use geo-coordinates as georeferencing system (coordinates WGS84), a button  will appear which will provide you with the possibility to set or correct the coordinates via Google Maps. Just click on the  button and a window will open with a map provided by Google Maps as shown below. If there are already coordinates provided by a different localisation e.g. by the DiversityGazetteer, these will be taken as a starting position. Thus, you may use an entry for a named area (DiversityGazetteer) as an approximate localisation and use additional coordinates for a more accurate localisation.

If you start with existing geographic coordinates (WGS84) in your data, the system will use these as starting point. You can zoom the map, drag it to another position and change from map to satellite mode. The actual position is symbolized by the  symbol in the middle of the map. The current coordinates are shown in the field at the bottom of the map. To include these coordinates in your data simply click OK.

With the Set start coordinates button you can set the coordinates which GoogleMaps should use as a starting position.

Please keep in mind that Google Maps coordinates are based on WGS84.

If there are no entries for the altitude and the named area, this data will be retrieved from the webservice ws.geonames.org and entered into the database. The source will be documented in the Notes field. Subsequent changes in the coordinates using the GoogleMaps function will update the altitude and named area entries provided they are derived from a webservice (ws.geonames.org) as documented in the Notes field.

Please keep in mind that the place names provided by ws.geonames.org may differ from those depicted in GoogleMaps.

To enter the localisations listed above simply enter the Coordinates WGS84. If an appropriate webservice is available (e.g. geonames) the Altitude and Named area will be added automatically.

Named areas - DiversityGazetter

The localisation system DiversityGazetteer is linked to the module DiversityGazetteer within the DiversityWorkbench and providing information on geographical names as shown below. The module DiversityGazetteer may contain several independent lists of geographical names, e.g. political and biogeographical regions. You therefore may add up to 5 links to the module DiversityGazetteer.

TK25 (MTB)

The source data for TK maps are stored in the module DiversityGazetteer. You need a access to a database of this module containing these data. If you choose MTB or TK25, the button will open a window where you can set the TK25 as well as the quadrant (see image below). Choose the quadrant depending on your preferred resolution. The thick line shows the current quadrant, the thin line the entire TK25. The needle in the center is placed at your current position. If you click on it, a message box will display the TK25 information as shown below.

If you click [OK], the TK25 values together with the coordinates of the center of the selected quadrant will be entered into the database.

Conversion of values

The values for any localisation system are stored in two text fields. You can enter your values as simple text. This may, however, prevent any calculations with said values. Thus, you should preferably enter your values according to the measurement units available. Whatever obsolete measurement units like feet or Fahrenheit may exist, within the DiversityWorkbench measurement data is stored in units according to the Système International d'Unités (SI). For those who still need to use these obsolete units DiversityCollection provides a possibility to convert them into their modern counterparts. To enter a numeric value choose the unit you prefer from the list. The form will change as shown below.

You can then edit the values and click on the  button to incorporate the changed values into your data. The system will calculate the corresponding value for storage in the database together with the default accuracy. You may correct this accuracy if you have more exact values. To indicate that the shown values are calculated from the values in the database the fields have a green background. When you save the data DiversityCollection will store geographic coordinates and the average altitude, if available, in separate fields.

The altitude, the exposition or the slope may be entered as one value or as a range of two values. If you use the conversion function and have only one value, make sure that the second field is empty.

Available units: meter and feet.

Available units: Orientation (N, NE, ... ) and degree rel. to North.

Available units: degree and percent.

The accuracy and uncertainty respectively will be calculated as an approximation in parts derived from Wieczorek, J. 2001 (MaNIS/HerpNet/ORNIS Georeferencing Guidelines. University of California, Berkeley: Museum of Vertebrate Zoology) and in parts according to Wieczorek, J., Q. Guo, and R. Hijmans 2004 (The point-radius method for georeferencing locality descriptions and calculating associated uncertainty. International Journal of Geographical Information Science 18: 745-767). The unit of the accuracy will always be the unit stored in the database according to the Système International d'Unités (SI) and degrees for angles respectively.

The data for the geography is stored in the table CollectionEventLocalisation.

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 add 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.

Transfer of selected data

To transfer all resp. the selected data into a specific sampling plot, choose

• Data
• Transfer
  • To plot…

from the menu. Several upcoming dialogs will guide you through the transfer.

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

Diversity Collection

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 DWB 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..