The image below gives you an overview of the main sectors related to the organisms.
Each specimen can contain several organisms and each organism may have been identified several times as shown in the image below.
To see the list of organisms within a Specimen, CollectionEvent, EventSeries or SamplingPlot use the taxon list function.
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.
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.
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.
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 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.
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).
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.
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.
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.
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.
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 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.
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.
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.