Animal reporting module

Extensions needed: animal reporting

Initial configuration

For the reporting system to function properly, it is recommended to perform the following steps before starting to use it. The configuration needs to be done by an admin.

1. Procedure severities and severity threshold

Admin / Codebooks / Severity

It is possible to define the levels of procedure severities used for reporting (higher number = higher severity). It is recommended not to change the predefined options unless legislation in your country requires that.

You can also specify the threshold severity value in Admin / Configuration, by changing the value of project.min_severe_procedure_level. By default, the threshold severity is mild.

• If the severity threshold is reached, animals will be subtracted from the Project capacity (see below for more details).
• If the severity threshold is not reached, the procedures will be reported in the report table but animals will not be subtracted from the capacity of the project.

2. Project

Projects / Dashboard

All current projects, running experiments, and the remaining project capacity are displayed in the Project dashboard.

Go to the new project form at Projects / Projects / Add project and add projects you wish to use for reporting.

It is mandatory to fill in a project code and a name, which will both be displayed in the project list. The code can be any combination of numbers and letters with a maximum length of 12 characters. Further mandatory fields include the leader and the deputy. Description, users, and expiration date are optional fields as well as the used fish limit. If set up, this limit will be displayed in the project dashboard in the color-coded horizontal bar below the project, where also the current usage of fish can be seen.

For each project, it is necessary to add the allowed experimental procedures that will take place within the project. Each procedure must have an associated maximum prospective severity selected from the drop-down menu. The number of procedures allowed in each project is unlimited - procedures can be added to a project by selecting add procedure. Also, new procedures can be created either straight in the form at Create new procedure, or in Admin / Codebooks / Procedure.

3. Age threshold

The minimum age when procedures need to be reported in a project can be set in Admin / Configuration in project.fish_reported_age. Typically, this is 5 dpf in zebrafish.

In case an experiment is launched with fish below the limit, their number will be subtracted from the corresponding project capacity, when the experiment is in progress. However, fish that have died before reaching the age threshold will no longer be counted as used fish after the experiment is finished. They will only be included and marked in the reporting table.

4. Observation period

To ensure that animals that have died as a consequence of a procedure are counted in an experiment, administrators can specify an observation period. The observation period is defined as the number of days that have to pass after a procedure, during which any deceased fish are still considered to die due to the experimental treatment.

By default, the observation period is set to 0 days. The administrator can change the length of the observation period in Admin / Configuration by changing the value of project.experiment_observation_period.

5. Burdens

In Zebrabase, burdens are genotype-zygosity combinations that are damaging to the animal, resulting in e.g. immunodeficiency, low survival, or a higher chance of cancer. It is possible to specify which genotype-zygosity combinations represent a burden for each fishline and should be tracked (see an example below).

Example of burdened genotype-zygosity combinations for fishlines with one and two genotypes - only some combinations produce the burden phenotype (marked by an exclamation mark):

To enter or edit burdens, go to a specific fishline record and click Edit burdens in the row Burdens. Then select all the genotype-zygosity combinations that represent a burden for the fishline. The table also contains these two options:

• ? - A burden is associated with undefined zygosity (i.e. before genotyping).
  
• Any - A burden is associated with all zygosities (but the substock has to be genotyped and positive in at least one allele).

Once you have the burdens defined, all substocks bearing the defined combinations will be marked as burdened by a red exclamation mark at the end of their name, so that you can distinguish them easily.

Burdened fishlines are confirmed in two steps: 1. Initial check is required for any newly added fishlines. It is accomplished by the steps described above. 2. The second check acts as a follow-up confirmation of the observations that should be performed after 3 generations of animals (the default interval in Zebrabase is 270 days, but can be changed). It should serve to capture any phenotypes that were not obvious during the initial stages of the breeding. You can keep track of the currently required checks on the admin dashboard.

In Admin / Configuration under the key project.default_burden_project, you can specify the default project for reporting burdened animals. In case a burdened substock does not have any project specified, it will be reported under the default project. If you need to report some animals under another project, these animals should be constantly associated with that particular project (not only during experiments).

You can also specify the key project.default_burden_severity to specify the default severity of burdens (the severity can be changed in the report form), and project.fishline_burden_check_interval, which is the default interval between the initial and consequent burden checks.

6. Configuration of count types

Changing the count type configuration is currently not permitted - this section is intended only for a better understanding of the mechanisms behind it.

Two attributes determine the input counts:

• count_to_experiment determines whether an input will be included in the project table (if a substock is not associated with a project, this attribute has no effect)
• count_to_burden determines whether fish that died during a given procedure should be added to used_burdened_fish of a project. If a substock is associated with an experiment and count_to_experiment is also set, then count_to_experiment will have priority over count_to_burden.

Admin dashboard

The admin dashboard allows for an easy visual check that your data is up-to-date. The five boards show the number of entries that should be reviewed by an administrator and potentially corrected. If there is no data to check, the displayed number will be a gray zero. Any red numbers should be reviewed. Clicking on the blue link at the bottom right corner of the boards will display the list of items to review.

1. Fishline burden initial check

In the initial check, any potential burdens should be entered for each new fishline or it should be confirmed that the fishline is not burdened. In the fishline detail, click the Edit burdens icon in the Burdens row, and this will allow you to select burdens for specific genotype-zygosity combinations. Clicking the green tick confirms the current status.

2. Fishline burden second check

After 270 days (i.e. 3 generations) of the existence of a new fishline, the fishline displays here, so that the original burdened status may be re-evaluated and corrected (removed or added) if necessary.
The delay between the first and second burden check may be changed in Configuration, key project.fishline_burden_check_interval.

3. Substocks of deleted fishlines

Only substocks of existing fishlines should be present in the database. This board will alert the admin in case a fishline has been deleted without the removal of associated substocks.

4. Projects exceeding expiration

Any projects running past the pre-set expiration date will be displayed here. They can be either deleted or their expiration date can be reset.

5. Project exceeding capacity

Any projects exceeding their capacity (i.e. the used fish limit) will be displayed here.

6. Project exceeding 75% of the capacity

Any projects exceeding 75% of their capacity (i.e. the used fish limit) will be displayed here.

Reporting the use of animals (for all users)

This section is intended for all users using the animal reporting module. It describes three scenarios:

1. Reporting of animals used in experimental procedures
2. Reporting of burdened animals
3. Reporting of special actions (e.g. genotyping)

1. Reporting of animals used in experimental procedures

STEP 1 - START A NEW EXPERIMENT

A new experiment can be started either from the Projects module or from a substock of your choice.

• From a substock: The detail of each Substock contains the Experiment action button, clicking on this button opens a drop-down menu where you can select between adding a substock to an existing experiment and designing a new experiment.
• From Projects: Go to Projects / Experiments and click on Add experiment.

In the new experiment form, the Name of the experiment and the Start date should be entered, as well as the Project this experiment will be a part of. The prefix of the experiment is generated automatically using the Project code and the Experiment number. Substocks are added to the experiment using the Add substocks field.

All currently running experiments and associated substocks can be viewed in Experiments.

STEP 2 - ADD SUBSTOCKS TO THE EXPERIMENT

This step needs to be completed only in case a new experiment has been started without adding substocks or if more substocks need to be added to an already running experiment - i.e. the substock you want to use in the experiment is not in the experiment yet. The associated substocks can be found in the Experiments overview, in the Substocks currently in experiment list.

Substocks can be added to experiments by clicking the Add to experiment action button in the substock detail and selecting Add to existing experiment.

Once the substock enters an experiment, all the following subtractive count actions will be reported and assigned to the experiment and project. It is not possible to euthanize an animal during the course of the experiment without an association of the count action to the experiment/project. If you wish to omit such an action from the experiment/project statistics, it is necessary to remove the substock from the experiment, euthanize the animals, and then add the substock to the experiment again.

When entering an experiment, all fish from a substock are added to the Used fish of the corresponding project. At the end of the experiment, the number is corrected based on how many animals were actually used. The animals are counted only if the severity of at least one of the procedures exceeds the defined threshold.

STEP 3 - REPORT AN EXPERIMENTAL PROCEDURE

To report an experimental procedure, use the action Count (Procedure) for the substock that is in the ongoing experiment. The new procedure can be added in the field Record new procedure; it is important to choose the correct Count type for each procedure based on the table below:

* Subtractive procedures subtract the number of fish on which they were performed from the total fish count of the substock.

For each procedure, it is necessary to enter:

• Count - how many animals have entered the procedure
  • For the option non-lethal procedure, it is recommended to enter All fish for the clarity of the record.
  • In case only a part of the substock is used for an experiment, it is recommended to split it first.
  • In case some animals will be marked as not used at the end of the experiment, the substock will be split automatically into a substock that underwent the procedures (and is reused) and another one that has not been used at all.
• The actual severity of the procedure
  • The Actual severity can be different than the prospective severity
  • Any severity with lower or the same level as the prospective severity is displayed in blue
  • Any severity with a higher level than the prospective severity is displayed in red
  • The default value corresponds to the prospective severity of the procedure

You can use the field Note to add a description of the action. The note will appear in the report table.

STEP 4 - REPORT ANIMALS AFTER A PROCEDURE

If animals are found dead or euthanized after a procedure, it is possible to associate them with the last procedure in the experiment. In that case, use the Count action and navigate to the “Add to existing procedure” part of the form.

STEP 5 - MULTI-PROCEDURE EXPERIMENTS

In case there are subsequent procedures in the experiment, steps 3 and 4 (reporting of procedures) can be repeated several times before leaving the experiment.

STEP 6 - ENDING AN EXPERIMENT

To remove a substock from an experiment, click the Leave experiment button in the substock record. When the only or the last substock is removed from the experiment, the user is asked whether he/she wants to terminate the whole experiment. An experiment cannot be terminated until all substocks leave the experiment first.

When leaving an experiment, it is possible to mark all or a portion of the surviving fish as unused. These animals will be subtracted from the Used fish of the project. A new unused substock will be split off from the original substock if only a portion of the fish is unused.

The overall severity of procedures can be reviewed and changed at this point. The default value is the highest severity the animals have experienced in the course of the experiment. However, it is suggested to use the maximum severity experienced by the animals throughout their life.

If an animal dies after the experiment has ended, the animal will not be counted in the experiment by default. However, it is possible to set an observation period, which will allow the users to report also animals that died soon after an experiment.

Animals that were used in a procedure with a severity higher than the threshold and left the experiment, but are still kept in the facility, are marked as Reused (recycle icon in the status bar and the name of the substock).

In case there are any Reused fish at the end of the experiment, a special type of procedure is produced in the Report table. This procedure includes the action Count with procedure severity equal to the maximum severity reached by any procedure the animals experienced (i.e. the overall severity).

2. Reporting animals with a genetic burden

It is not necessary to start an experiment to report burdened animals under a project. Instead, they can be reported directly under a chosen project and they will appear in an independent section, similar to genotyping reports. Animals will be counted automatically in case a subtractive count (died/euthanized) is saved for the burdened substock (see below) and the substock has a Project assigned.

When reporting dead or euthanized burdened animals, the severity of the procedure must be selected. The default severity for burdened animals is mild but it is possible to reconfigure this for the whole database of the facility (in Admin / Configuration at project.default_burden_severity).

A new project dedicated to reporting burdened fish can be created and used in these cases.

3. Reporting genotyping

Similarly to burdened animals, genotyping can be reported under a project without creating an experiment. In the form for the Genotyping action, there is a section where you can directly select the project which should be used for the reporting, and the method.

4. Batch actions for substocks in the experiment and burdened substocks

There are certain limitations of batch actions for substocks with a burden or in an experiment. Using Count and Terminate should be avoided in the batch mode if the substock is burdened or in an experiment. These actions will not be accepted because they require an input of specific details (e.g. procedure severity).

However, it is possible to use the advantages of the batch mode for other actions, e.g. removing substocks from an experiment, changing the productivity, conditions, etc.

Reports

Each project has a variable used_fish which sums up all fish used in this project (any procedure severity). The value is displayed on the fish usage indicator bar, and also in the field Fish usage in the project detail. In the project detail, you can also find itemized the 3 constituents of fish usage: experiments, burdened animals, and genotyping.

For each project, an overview of all experiments and used burdened animals can be seen at the bottom of the page in project detail. It consists of three parts: Experiment report, Burdened fish report, and Genotyping report. The reports consist of list of all experiments and procedures, and a summary (for each year and the whole project), which contains the used fish counts according to:

• EU - the current EU legislation (each animal is only used once, the highest procedure severity is counted)
• all - overall summary (each procedure is counted, one animal can be counted multiple times)

Experiment report

The table of experiments for each project is generated from Count inputs and offers a detailed overview of the use of fish in the project.

The numbers of animals undergoing different levels of procedure severity are summarized for each experiment and also for the whole project. The number of unused animals is also specified for each experiment - this only applies if the animals are set as unused when the substock is exiting the experiment and there are still some animals alive.

Burdened fish report

Breeding fish with burdened phenotypes should be always reported (according to the current EU legislation).

This table shows all burdened animals that died under the project and the associated severity. If the burdened lines are not already entered in another project, we recommend setting up a dedicated project for reporting burdened fishlines. The default project for reporting burdens can be set in Admin / Configuration under the key project.default_burden_project.

Genotyping report

Similarly to burdened fish, all genotypings are automatically reported in a separate table. For fish that are not a part of any specific project, we recommend setting up a genotyping project, under which the genotyped fish will be reported. You can change the default project for reporting genotypings in Admin / Configuration under project.default_genotyping_project.