Subsections of Tutorial
Tutorial Creation
Tutorial - Creation of a new data set
For an introduction see a short tutorial
.
To enter a new data set click on the
button in the upper left panel (see point 1 in image
below). In case of accession numbers being available in the database,
the software will ask whether you wish to take the next free number (see
accession for further information). If you click on the
OK button, the program will try to find the next free accession number
starting with your current accession number.
Finally you will find a new entry in the specimenlist on the left and the trees for the
specimen (see point 2 in image below) and the
storage as shown below.
If you did not specify an accession number, the entries will look like
in the image above. Otherwise the accession number will be shown. To
enter your data for the specimen click on the entry in the upper tree as
shown below (see point 3 in image below). This will open the fields
where you may enter the details for the specimen in the area on the
right of the tree (see point 4 in image below).
In the panel in the middle of the form several buttons will appear where
you may enter additional information for this specimen.
With these buttons you may enter information for the:
This tutorial is continued in the sections listed below.
Tutorial Project
Tutorial - Project
To set the accession number for the CollectionSpecimen select it in the
overview (see point 1 in image below) and enter the accession number
(see point 2 in image below).
Project
To restrict the access to your data set add it to a project (click on
the button - see point 4 in image above). A
dialog will open where you may select a project from the projects
defined in DiversityCollection (see image below). The project will then
be added to the list of the projects for this specimen.
This tutorial is continued in the sections listed below:
Tutorial Event
Tutorial - CollectionEvent
To enter information about the CollectionEvent (when and
where the specimen was collected) click on the 
button (see point 1 in image below).
This will add an entry for the CollectionEvent in the upper tree as
shown below. Select this entry in the tree (see point 2 in image
below) to open the fields for the CollectionEvent. To see the projected
contents of any data field simply place your mouse in the field. An
explanation will appear as for the field Description of the
locality:
See the Event part for further details.
Then enter the date (see point 3 in image below) of the
CollectionEvent. If you click on the drop-down button as shown in the
image below, a calendar will open where you may select the date. Then
enter the description of the locality (see point 4 in image below).
To store the data entered so far click on the 
button (see point 5 in image below).
Now you have the possibility to enter more details about the locality
like coordinates, named places, etc. by clicking on the
button (see
point 6 in image above).
This tutorial is continued in the sections listed below.
Tutorial Localisation
To enter more information on the CollectionEvent like
coordinates, named places, etc. click on the
button (see image below).
Now you may select an option from the following list:
The three most important options are:
New Coordinates WGS84
You may add the exact coordinates for the locality with the assistance
of Google Maps. Click on the button (see
first image of this site) and choose New Coordinates WGS84 (Google
Maps uses WGS84). This will add a new entry in the overview. Select it
(see point 1 in the image below) to open the details for this entry.
Here click on the 
button (see point 2 in image below).
A window will open as shown below where you may set the coordinates
simply by dragging the map with your mouse. The coordinates correspond
to the center of the map, symbolized with the
. Click on the OK button to store the
coordinates.
In the main window the coordinates will be stored at two positions - see
image below. In the upper area you may set the values and choose a
different format for display as shown here - the more familiar form with
degrees, minutes and seconds. Change the values and click on the
button to change the original entry. At the same
time the numeric values are stored in fields which can not be edited by
the user (see below).
New Named Area (Diversity Gazetteer)
To enter a name of a place using the DiversityGazetteer choose New
Named Area (DiversityGazetteer) from the list. In the overview tree in
the middle of the window an entry will be inserted as shown below.
Select it to open the detail fields for this entry (see point 1 in
image below).
To open the connection to the DiversityGazetteer click on the
button (see point 2 in image above). A
window will open as shown below. Enter a search string - for example the
city you wish to find (see point 3 in image below) - and start the
query with a click on the 
button (see point 4
in image below).
In the middle of the form the results of the query will be listed.
Select one of these. To guide you to the correct entry details to this
place are listed in the area right of the list. The base will show a map
corresponding to the coordinates connected to this entry. After
selecting the correct entry (see point 5 in image above) click on
the OK button to return to the main window (see point 6 in image
above). As shown below the data retrieved from the gazetteer will be
written in several areas. Next to the name of the place the
DiversityGazetteer provides the coordinates and the country as shown
below.
The area where you entered the name now changed to a locked state and
will prevent you from changing the entry (see image below). Next to the
field with the place you find the link to the external module.
Double-click it for more details.
If you wish to remove the connection to the external module click on the
button. This will keep all entries (country,
place, coordinates) but remove the connection to DiversityGazetteer.
New Altitude (mNN)
As last information about the locality we enter the altitude. Click on
the button (see first image of this site)
and choose New Altitude (mNN) (see point 1 in the image below).
Select the new entry in the overview to open the data fields (see point
2 in the image below). Let’s suppose you have only feet values
available - change the display format to feet (see point 3 in the
image below). Enter your values (see point 4 in the image below) and
click on the button (see point 5 in the image
below) to save your entries. Now your values are converted to meter (the
internal format of DiversityCollection) automatically. If you now change
the display format to meter, you can see the result. The program
calculates an average value for the altitude and accuracy in meter
corresponding to the accuracy of your original values (see below). The
original values of your entry are saved in the Notes field.
This tutorial is continued in the sections listed below.
Tutorial Event Series
If you wish to organize your CollectionEvents, you may use the
CollectionEventSeries. To create a new EventSeries select the
ColletionEvent (see point 1 in image below) and click on the
button (see point 2 in image below).
In the tree the entry for the new EventSeries will appear (see point
3 in image below). Select this entry in the tree to enter the
details about the EventSeries (see point 4 in image below).
To build a hierarchy for your CollectionEvents and CollectionEventSeries
choose the created EventSeries in the tree (see point 1 in image
below) and create a new secondary EventSeries (see point 2 in image
below).
Then enter the date of the CollectionEventSeries. If you click on the
drop-down button as shown in the image below, a calendar will open where
you may select the date. Then enter the description of the locality. To
store the data entered so far click on the button.
Select the entry of the new EventSeries (see point 3 in image below)
and enter the details of the EventSeries (see point 4 in image
below).
Finally drag the CollectionEvent to its position within the hierarchy of
the CollectionEventSeries entries (see point 5 in image below).
To include an existing event in a hierarchy of the CollectionEventSeries
select the CollectionEvent and click on the
button. For more details see the
section CollectionEventSeries.
This tutorial is continued in the sections listed below.
Tutorial Specimen
To set the accession number for the CollectionSpecimen select it in the
overview (see point 1 in image below) and enter the accession number
(see point 2 in image below).
To search for the next free accession number click on the corresponding
button as shown above (see point 3 in image above). A window will
open as shown below. Start the search for a free accession number. If
the query ended successful, click OK to include the new accession
number in your data set.
Project
To restrict the access to your data set add it to a project (click on
the button - see point 4 in image above). A
dialog will open where you may select a project from the projects
defined in DiversityCollection (see image below). The project will then
be added to the list of the projects for this specimen.
This tutorial is continued in the sections listed below.
Tutorial Collector
Collectors
Now we will add the collectors of the specimen. In the overview select
the specimen and click on the 
button to insert a
new collector (see point 1 in image below). Select the collector in
the overview (see point 2 in image below). Now we use the module
DiversityAgents to search for a certain person. Click on the
button to open the interface of the
module (see point 3 in image below).
In the interface for DiversityAgents enter search criteria (see point
1 in image below) and click on the button to
start the query (see point 2 in image below).
Select the correct entry from the query result (see point 3 in image
above) and click on the OK button (see point 4 in image above) to
store the name in DiversityCollection.
The next collector will have no connection to the module
DiversityAgents. To insert this collector click on the
button again (see point 1 in image below) and
select it (see point 2 in image below). Type the start of the name
in the field for the name (in this example “Mei” would be a good choice)
and click on the drop-down button 
(see point
3 in image below) to select a name from the list of collectors
already stored in the database. Finally if the collector has a field
number, enter said number (see point 4 in image below).
This tutorial is continued in the sections listed below.
Tutorial Relation
There are two types of relations possible:
- relation to a specimen within DiversityCollection
- relation to a specimen not administrated in the local database.
1. Internal relations
To enter a relation to a specimen in DiverisityCollection select the
specimen in the tree (see point 1 in image below) and click on the
button (see point 2 in image below).
A window will open where you can search for the related specimen. In the
window enter your restrictions (see point 1 in image below) and
start the query (see point 2 in image below). Select the related
specimen from the result list (see point 3 in image below) and click
OK (see point 4 in image below) to insert the relation.
In the window select the entry for the relation (see point 1 in
image below) to display the fields for the details. Then enter the type
of the relation (see point 2 in image below).
2. External relations
To enter a relation to a specimen in a foreign collection insert a
relation (see point 1 in image below) and select it in the overview
(see point 2 in image below). Enter the name of the specimen (see
point 3 in image below) and the type of the relation (see point
5 in image below).
If there is a data set for the collection available you may select it
from the list (see point 4 in image above). Otherwise you first have
to add this collection to the list. If you have permission to edit the
collections, choose Administration -> Collections from the menu to add
a collection. See the section Collection for details.
For further information on relations turn to the section
Relation.
This tutorial is continued in the sections listed below.
Tutorial Unit
To focus on the specimen and its organisms hide all other entries from
the tree by clicking on the corresponding buttons (see point 1 in
image below). To enter the organism choose the
specimen entry in the tree (see point 2 in image below). Then select
the organism from the 
list.
This will insert an entry for the organism
underneath the entry of the 
specimen (see image
below). To enter details for this organism select the entry in the tree
(see point 3 in image below and image above).
To enter an identification for this organism select it in the tree (see
point 4 in image above) and click on the
button (see point 5 in image above).
This will insert a data set for the identification of the organism
underneath the organism as shown above. Select this entry to enter the
details of the identification.
To enter more organisms living on the plant select the
plant in the tree (see point 1 in image below)
and create new organisms as described above (see point 2 in image
below).
Now let’s enter the taxonomic name of the plant. Select the entry for
the identification in the tree (see point
1 in image below). As a simple method to enter a taxonomic name
simply type it in the field Tax. name (see point 2 in image
below). To save the data set and display the taxonomic name in the tree
click on the button (see point 3 in image
below).
Now insert an identification for the
fungus (see point 1 in image below).
Select the identification in the tree and click on the
button (see point 2 in image
above) to open a remote query as shown below.
Choose the database DiversityTaxonNames_Fungi (see point 1 in image
below), enter the conditions for the query, e.g. the beginning of the
taxonomic name (see point 2 in image below) and start the query
(see point 3 in image below). From the result
list select the taxonomic name (see point 4 in image below) and
click OK (see point 5 in image below) to transfer the selected name
to the main form.
The name of the selected taxon together with the link to the datasource
(see image below) will be inserted in the field for the taxonomic name.
The taxonomic name can not be directly edited as long as the name is
linked to a datasource (indicated by the yellow background). To remove
the link you need to use the button. To see the
entire information on the linked name as stored in the datasource click
on the button.
As an example for the last variant enter an identification for the
insect (see below). Select the identification in the tree (see point
1 in image below) and click on the
button (see point 2 in image
below) to open a remote query.
A window for the access to webservices and other modules will open as
shown below. Here select CatalogueOfLife (see point 1 in image
below) as a datasource. This will query the webservice of Catalogue ofLife for a taxonomic name.
Enter the beginning of the taxonomic name (see point 2 in image
below) and start the query (see point 3 in
image below). From the result list select the taxonomic name (see point
4 in image below) and click OK (see point 5 in image below) to
transfer the selected name to the main form.
The name of the selected taxon together with the link (see image below)
to the data source will be inserted in the field for the taxonomic name.
The taxonomic name can not be directly edited as long as the name is
linked to a data source (indicated by the yellow background). To remove
the link you need to use the button. To see the
entire information on the linked name as stored in the data source click
on the button.
This tutorial is continued in the sections listed below.
Tutorial Storage
To enter the data connected with the storage of the specimen
click on the 
below the specimen tree. A window
will appear where you have to select the material category of the part
you want to insert (see below). In the list select “herbarium
sheets”.
Another dialog will appear where you are required to enter the
collection where your specimens are stored (see below).
Select the collection from the list or the hierarchy and click OK to
close the dialog. The bottom tree will now contain the selected material
with all organisms (see below).
Let’s assume that the insect is not present in the specimen, but e.g.
has only been observed during the collection of the sample. To document
this remove the entry for the insect from the Show in label list to
the Units not in part list: Select it (see point 1 in image
above) and remove it (see point 2 in image above) (click on the
< button). The result is shown below.
To see the exact position within the collection click on the
button at the left side of the tree. The tree
will change as shown below where all the collections and subcollections
together with the parts of the specimen are listed (see below).
To print a label for a stored part of the specimen select it in the tree
(see point 1 in image below) and click on the 
button in the upper right corner to open the area for the label (see
point 2 in image below). Click on the 
button
(see point 3 in image below) to select a Schema file (e.g.
Standard.xslt). Then click on the 
button to
generate a label (see point 4 in image below).
Turn to the Section part for more details.
This tutorial is continued in the sections listed below.
Tutorial Query
To search for data in the database use the query sector in the left part
of the window. To select the query conditions click on the
button in the top panel. A window will open as
shown below.
With the Maximum number of results you may limit the package size
which should be retrieved from the server. For a slow connection to the
database server choose a low value (e.g. 100 as set by default).
The Limit for drop-down lists restricts the maximum number of
drop-down lists which should be created. For a slow connection to the
database server choose a low value. The default is set to 0 which means
no drop-down lists will be created.
Click on the Check none button to clear the previous selection. Then
select the entries
- Project -> Project
- Specimen -> Accession number of specimen
- Specimen -> The user who created the data set
- Specimen -> The date when the data set was created
- Event -> Collection date
- Organism -> Organism present
- Organism -> Only observed
- Storage -> Material category
- Image -> Type
Click OK to close the window. Your query conditions will be displayed as
in the image below.
Project -> Project: Here you may choose from a list of possible
entries. Select your current project.
Collection specimen -> Acc. Nr.: From the operator drop-down list
choose “~” and enter the first letters of your accession number. You
may include wildcards. Other options are e.g. “-” for a
range or “>” for a lower limit. The conditions will be interpreted as
text! So 2 will appear after 10 etc.
Collection specimen -> Creat. by.: From the operator drop-down list
choose “=” and choose your user name from the list.
Collection specimen -> Cre. dat.: From the operator drop-down list
choose “=” and choose the current date with the help of the calendar.
Collection event -> Date: >From the operator drop-down list choose
“=” and enter the current year in the last field.
Organism -> Presence: From the operator drop-down list choose “•”
which means that an organism is present.
Organism -> Only obs: Uncheck the checkbox to find organisms which
were not only observed.
Part of a specimen -> Mat.cat.: Use the 
button on the right of the combobox to open the hierarchy and select
“herbarium sheet”.
After all query conditions are set, click on the
button to start the query. In the result list you should find the
specimen created in this tutorial. To save your current query click on
the 
button on the right of the
button. A window will open as shown below.
For more details see the section Save query.
button or choose
Connection -> Database… from the menu. A window will open where
you may enter your account information and choose the database (see
image below, for further information see databaseaccess). See a short
symbol in the right upper corner, you are now
connected to the database. The tooltip of the 