workbook.qmd

# Description of the Workbook

## Module organization

The individual modules (i.e. sheets) of the excel workbook are given a name and the purpose of the sheets is explained below. 
There might be two or more analytical (measurement) endpoints to establish a primary endpoint, therefore 'n' refers to the number given to different assays (assays to measure LDH release, resazurin reduction, ATP levels can be given numbers as Assay-1, Assay-2, Assay-3 respectively for assessing the toxicological endpoint related to cell viability).

**Modules:**

* The **Project** module connects the studies within the specific WP5 project
(i.e., via the project description) and other details, e.g., name of the
project leader(s), Organisational affiliation of the Project Leader(s),
name of the person who can be contacted.
* The **Action** module is a unit of research and contains contextualising
information about one or more assays.
* The **Assay** module contains information about a set of assays, defined by
the endpoint measured (e.g., increase in cytokine expression) and the
technology employed (e.g. ELISA). The worksheet also describes the
protocol followed and contains references to raw and processed data
files (and their locations). There might be two or more analytical
(measurement) endpoints to establish a primary endpoint, therefore
additional assay files/excel sheets can be created for each of the
different assays (such as, assays to measure LDH release, resazurin
reduction, ATP levels for assessing endpoint related to cell viability).
* The **TestSubstance** module contains overall information of the test
chemical (s) tested in the project.
* The **PositiveControl** module contains information on the positive controls
used in the assay(s). (This sheet follows the descriptions provided in
the *TestSubstance* module).
* The **NegativeControl** module contains information on the negative controls
used in the assay(s).
* The **AssaySummaryResult** module contains the reporting template for the
summary data to be reported for a particular assay. For additional
assays, additional worksheets are suggested to used with sheet tab name
as summary-assay-1, etc.

**Field Type:**

- **Mandatory (M):** The metadata element shall be documented. These
  fields are necessary for findability, provenance, proper data
  analysis, and reuse. Please ensure all information is entered
  accurately.
- **Recommended (R):** These properties are strongly suggested to be
  included in order to provide more insight into your meta(data).
- **Conditionally required (C):** The metadata element shall be
  documented if a previous element has been documented/recorded
- **Optional (O):** Provided to allow users to document their data in an
  enriched manner. Leave it blank only if it is very challenging to
  provide a response to a particular field. It is advised to provide as
  much detail as possible for completeness, QC/QA, and reproducibility.

This document is a generic template in the sense that some of the fields
may not be applicable to all toxicological experiments (e.g.,
pre-treatment, cell defining features), and in some cases, additional
fields (e.g., differentiation status of cells in the case of
immunotoxicity experiments) may be considered. Hence, the guide to fill
the fields will be customised as per the (meta)data reporting template.
Some information is routinely reported in publications, whereas some
others are non-formalised (e.g., measured concentrations, lot/batch
number) part of experiments, and hence generally not reported. Within
each tab of the excel sheet, some of the fields (e.g., positive control,
additives) are part of the general set-up of experiments and hence the
way the information is asked for when filling it could be tedious.

Varied efforts exist (some in parallel) regarding toxicity meta(data)
and consistency in definitions is yet to be achieved, therefore, we have
specified the meaning of several terms while describing the field names,
and wherever they have been taken from published resources (or where
ontologies exist, even if overlapping efforts are there, e.g.,
[Foundation Model of
Anatomy](https://bioportal.bioontology.org/ontologies/FMA) and
[UBERON](https://obophenotype.github.io/uberon/) for anatomy) the
reference / and ontology source of the chosen term is provided within
the description provided in the guidance document.

Each of the sheets in the (meta)data reporting template encompasses
descriptive, administrative, quality, and provenance metadata types.

## Field details

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## Ongoing vs closed projects
There are differences in the Mandatory fields between ongoing projects and closed projects ({{< var closed_def >}}).
:::

To view field details for the workbook modules click the appropriate button below:

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[Ongoing projects](/ongoing.qmd){.btn-action-primary .btn-action .btn .btn-lg .w-100 role="button"}
:::
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[Closed projects](/closed.qmd){.btn-secondary .btn-action .btn .btn-lg .w-100 role="button"}
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