The DiversityWorkbench is a set of components for building and managing biodiversity information, each of which focuses on a particular domain.
In the figure shown below the connections to other modules within DiversityCollection are indicated.
The DiversityWorkbench is a set
of components for building and managing biodiversity information, each
of which focuses on a particular domain. DiversityAgents is referred by
several modules. To scan for references from these modules on data in
DiversityAgents choose Data - Scan modules -
from the menu (see image below).
With these options the program will scan all sources of the selected module as listed in the connections for references to the current agent. After selecting an agent in the tree, the sources of the selected modules together with the linked data will be listed as shown below.
Select a link to see a summary of the linked data (see below).
To get further information about an item click on the
button. If so far the path to the
respective application has not been set, you will get a corresponding
message (see below).
Click on the 
button to set the path to the
application (see below).
By default the path to the application is C:\Program Files (x86)\DiversityWorkbench\Diversity...\Diversity.…exe as shown.
The DiversityWorkbench is a set of components for building and managing
biodiversity information. Each of which focuses on a particular domain
and provides services for the other modules. For an
introduction see a short tutorial
.
To use the service of an external module you need access to the database of this module and optionally the module application placed in your application directory. Entries related to an external module have a standard interface in the main form.
There are 4 options to link the content to a datasource (or module).
Local database
Remote database
Cache database
WebserviceThere are two differnt approaches for providing content for the textbox. Either as a
autocomplete list (, ,
) or by searching values on base of the entered text in combination with a combobox ().
For the autocomplete lists just start to type and the corresponding entries will
be listed where you can choose the entry you are looking for. To set the
link including additional information provided by the original source
(, ), you just have to leave the textbox. The program will then contact the database to which the entry corresponds and insert the additional information including the link to the source database.
The next paragaphs show how to uses this linking. The colours of the pins are automatically set when a datasource is set. The colour indicates if the current set datasource ist set to the local, remote or cache databse or to a webservice.
To select one of the datasources, click on the button and choose among the sources.
The values shown in the autocomplete list are taken from the entries in
the local database.
This is the default. To refresh the content or slect the local databse as source, click
on the pin button, choose the first empty entry of the list
and click OK.
To set the datasource on a remote database, choose a database from the
list.
Either a database available via a linked server (e.g. [TNT.DIVERSITYWORKBENCH.DE,5432].DiversityTaxonNames_TaxaVaria see below) or a database on your local
server, starting with e.g. DiversityTaxonNames for taxa in the identification
Next you will be asked to choose a project within the selected source.
In case there are additional options you may be asked e.g. for taxa to
restrict the content to a checklist provided by the datasource. The
pin button and the textbox will change their
color to orange to indicate the current source type.
The autocomplete list is then generated based on the content in the
remote database. When you leave
the textbox the software will automatically add additional information from the selected source and
set the link as shown below.
To provide data via the cache database these data must be first imported as
source as described in the link to cacheDB chapter.
This option
provides faster access to remote data e.g. on linked
servers 
. To choose a
source from the cache database, click on the
pin button and select the entry CacheDB from the list (see below) and click
OK.
Next you will be asked to choose among the sources provided by the cache
database. Choose your preferred source and click OK. The
button and the textbox will change their
color to to indicate the current source type. Now
the values for the autocomplete list will be based on this datasource.
Just start to type and the corresponding entries will be listed where
you can choose the entry you are looking for. To set the link including
additional information provided by the original source, you have to
leave the textbox. The program will contact the database to which the
entries in the cache database correspond and insert the additional
information.
To set the datasource on a webservice, choose a webservice from the list
as shown below. The pin button and the textbox
will change their color to blue to indicate the
current source type.
To get data from the webservice, you have to enter a search text in the
textbox and click on the combobox 
button to search the
webservice for matching entries. Choose among the provided results to
fill the textfield and the set the link to the webservice.
There are several states and functions of this interface:
1: the value is only set in the local database with no connection to the remote module. In this state you may either type the value or select it from the values which are already available in the database (see above).
2: the value is related to the remote module.
If you wish to set a relation to the remote module you have 2 options:
Click on the pin button to select a
source as described above.
An overview for all settings can be found under Administration - Customize display - Settings.
After the source is set to a database of the DiversityWorkbench certain
datasources provide also charts for the selection of taxa or terms. Click on
the 
chart button
to open a table where you can select one of the provided taxa resp.
terms.
Click on the amonite button. A
window will open where you may select an entry from the foreign
database. If the option for loading the
connections is not set the connection to a database
may not be established indicated by a 
button.
Either requery all connections as described in chapter
Connections or click on the
button to open the database connections for
the linked module. With this option you have the full range of query
options as shown in the image below as well as access to additional
webservices.
For DiversityScientificTerms you can use a hierarchy for the selection of the lists as shown below.
If the value has a relation to the remote module, the interface will appear as shown below with the content of textbox set to read only and a yellow background.
To release the connection to the remote module click on the
button. If you require further information on the
value, click on the button. This will
open a form showing an overview of the related value.
If the client application of the module is available, you may inspect
the details of the entry. To start the client application of the remote
module click on the button.
If the provided link does not correspond to a dataset in the source, you
will get a message as shown below. Click Yes to remove the wrong link
and replace it with a valid
link.
Some modules provide the possibility to link your data to an external
webservice. For example, DiversityTaxonNames gives you access to the
taxonomic names of IndexFungorum. To establish a connection to an
external webservice click on the
button. As with the link to modules within the DiversityWorkbench, a
window will open where you are able to choose from either
DiversityWorkbench modules or external Webservices. See
chapter Webservice for further details
Some modules within the DiversityWorkbench provide the possibility to
link your data to an external webservice. For example
DiversityTaxonNames gives you access to the taxonomic names of Index
Fungorum. To establish a connection to an external webservice click on
the button. A window will open where
you may choose from either DiversityWorkbench modules or external
Webservices. For an overview see a short tutorial
.
The currently provided webservices are:
DiversityWorkbench provides the possibility to link your data to an
external webservice. The webservice provided by the Catalogue of
Life is possible through the
module DiversityTaxonNames. To establish a connection to this external
webservice click on the button. A
window will open where you may choose this webservice (see below).
In the field Name in Query conditions enter your search string and
click on the 
button to start the query. In the
list of the left upper part the results of the query will be listed. In
the right part of the window additional information is shown as provided
by the webservice.
To include the link from the webservice into your
database choose one of the entries in the list and click OK. The entry
will change as shown below.
If you double-click on the link area, a window will open providing you with the retrieval information of the webservice (e.g.:https://api.checklistbank.org/dataset/3LR/nameusage/8K9Y).
To receive the information related to an entry as provided by the
webservice click on the 
button. A
window will open as shown below where information on the webservice is
listed in the upper part. If available, additional information provided
on a corresponding website will be shown in the lower part.
If you wish to remove the link to the webservice, click on the
button. This will only remove the relation to the
webservice, not the cached name.
Some modules within the DiversityWorkbench provide the possibility to
link your data to an external webservice. For example
DiversityTaxonNames gives you access to the taxonomic names of Index
Fungorum. To establish a connection to this webservice, click on the
button. A window will open where you
may choose Index Fungorum from the database list (see below).
Enter the query restriction for the name in the Name field in Query
conditions. The maximum number of records you receive may be set in the
max. results field 
(choose a low
number, if you have a slow connection to the internet). Click on the
search button to start the query. In the list in
the left upper part the results of the query will be listed. In the
right part of the window additional information is shown as provided by
the webservice. For certain entries buttons will appear, as e.g. shown
above for the basionym and the current name of a scientific name. Click
on these buttons, if you wish to change to one of these related data
sets from the webservice. If available, the information provided on the
corresponding website is shown in the lower part. To include the link
from the webservice into your database choose one of the entries and
click OK. The entry will change as shown below.
If you double-click on the link area
, a window will open providing you with the retrieval
information of the webservice.
To receive the entire information related to this entry as provided by
the webservice click on the button. A window will
open as shown below where information on the webservice is listed. If
available, the lower part will show the corresponding information of a
website.
If you wish to remove the link to the webservice, click on the
button. This will only remove the relation to
the webservice, not the cached name.
DiversityWorkbench provides the possibility to link your data to an
external webservice. The webservice provided by the Palaeontology
Database is possible through the
module DiversityTaxonNames. To establish a connection to this external
webservice click on the button. A
window will open where you may choose this webservice (see below).
In the field Name in Query conditions enter you search string and
click on the button to start the query. In the
list of the left upper part the results of the query will be listed. In
the right part of the window additional information is shown as provided
by the webservice. The lower part of the window will show the webpage of
the related information.
For synonyms the accepted name will be shown as well as shown above. To change to the accepted name click on the linked entry of the ID - in the example above ID: 57254. To include the link from the webservice into your database choose one of the entries in the list and click OK. The entry will change as shown below.
If you double-click on the link area
, a window will open providing you with the
retrieval information of the webservice.
To receive the information related to an entry as provided by the
webservice click on the button. A
window will open as shown below where information on the webservice is
listed in the upper part. If available, additional information provided
on a corresponding website will be shown in the lower part.
If you wish to remove the link to the webservice, click on the
button. This will only remove the relation to the
webservice, not the cached name.
Some modules within the DiversityWorkbench provide the possibility to
link your data to an external webservice. For example
DiversityTaxonNames gives you access to the taxonomic names of the
Pan-European Species directories Infrastructure (PESI). To establish a
connection to this webservice, click on the
button. A window will open where you
can choose PESI from the database list (see below).
Enter the query restriction for the name in the Name field in Query
conditions. Click on the search button to start
the query. In the list in the left upper part the results of the query
will be listed. On the right part of the window additional information
is shown as provided by the webservice. If available, the information
provided on the corresponding website is shown in the lower part. To
include the link from the webservice into your database choose one of
the entries and click OK. The entry will change as shown below.
If you double-click on the link area
, a window will open providing you with the retrieval
information of the webservice.
To receive the entire information related to this entry as provided by
the webservice click on the button. A
window will open as shown below where information on the webservice is
listed. If available, the lower part will show the corresponding
information of a website.
If you wish to remove the link to the webservice, click on the
button. This will only remove the relation to the
webservice, not the cached name.
The module DiversityReferenes gives you access to the webservice Recent
Literature on Lichens. To
access this service click on the
button. A window will open where you can search for entries in the
database (see below).
Enter the query restriction for the Authors, the Year and the
Title in the query conditions. Click on the search button
to start the query. In the list in the left upper
part the results of the query will be listed. On the right part of the
window additional information is shown as provided by the webservice. To
include the link from the webservice into your database choose one of
the entries and click OK. The entry will change as shown below.
If you double-click on the link area
, a window will open providing you with the retrieval
information of the webservice.
To receive the entire information related to this entry as provided by
the webservice click on the button. A
window will open as shown below where information on the webservice is
listed.
If you wish to remove the link to the webservice, click on the
button. This will only remove the relation to the
webservice, not the cached name.
In the module DiversityDescriptions you can link data to
DiversityCollection. To detect these links and list them in
DiversityCollection, select the specimen 
in the
tree and activate the checkbox 
Scan module
DiversityDescriptions at the bottom of the details
section. If there are links found in the available DiversityDescriptions
databases, these will be listed as shown below. Select one of the items
in the list to show some basic data stored in DiversityDescriptions (see
below).
To show the details in the module DiversityDescriptions set the path to
the application (click on the button) and
click on the 
button. The module
DiversityDescriptions will start, showing the dataset with the link to
DiversityCollection (see below).
