"Data Collection Toolkit" refers to H3ABioNet's set of
harmonised standards and reusable modules for collecting
clinical phenotype and exposure data in genomics studies. It is
not a single piece of software — it's a curated combination of
standards, ontologies, and pre-built data-collection forms.

What's in the toolkit:

• Phenotype-specific data collection modules. Developed
  with the H3Africa Phenotype Harmonisation Working Group,
  these are reusable form templates and standardised variable
  definitions for common disease areas (cardiometabolic,
  infectious disease, cancer, etc.). The intent is that
  studies across the continent can collect comparable data,
  which makes downstream joint analyses possible.
• REDCap as the collection tool. H3ABioNet provides
  support for REDCap and recommends it as the primary data
  capture platform. See
  https://www.afrigen-d.org/data-resources#data-collection-toolkits.
• PhenX-based protocols. Where appropriate, modules draw
  on the international PhenX Toolkit
  (https://www.phenxtoolkit.org) for consistent measurement
  protocols.
• Standardised consent codes (GA4GH DUO). Datasets are
  tagged with Data Use Ontology terms so downstream consumers
  can computationally check that their intended use matches
  the consent.
• GECKO ontology for cohort description. Standardises how
  cohorts are described so they can be discovered and compared
  across studies.

Why it matters:

• Without harmonised collection, joint analyses across studies
  become impossible — you can't pool data when one study
  collected blood pressure with two readings and another with
  three.
• DUO-tagged consent means future data-access decisions can be
  made consistently and at scale, including by automated tooling.
• Studies that follow H3ABioNet standards have a much easier
  path to publishing their data via the H3Africa catalogue
  and EGA, because the metadata aligns with what the catalogue
  expects.

How to use it for your study:

1. Read the overview at
   https://www.afrigen-d.org/data-resources
   and the standards page at
   https://www.afrigen-d.org/data-resources.
2. Decide which phenotype modules you need (disease area
   specific). If your area isn't currently covered, raise a
   helpdesk ticket — the Phenotype Harmonisation Working Group
   may already have an in-progress module, or your study could
   feed into the next iteration.
3. Set up REDCap (or get access to your institution's
   H3ABioNet-supported REDCap instance — see the REDCap queue
   for access requests).
4. Import the relevant data dictionary / module template,
   adapt to your study, and validate against the standards.
5. Tag your datasets with appropriate DUO consent codes from
   the outset — much harder to do retrospectively.

Where to get help:

Raise a helpdesk ticket in the Data Collection Toolkits
queue with: your study design (briefly), the phenotype area
you're collecting on, and your REDCap status. The data
standards team will route you to the right module or
collaborator.