Data Standardisation

H3ABioNet provides guidelines on the use of clinical data, data management and data standardization

Data & Standards

Data Standardisation

H3ABioNet’s efforts surrounding data collection and curation involve the promotion of standardised data collection processes across H3Africa and the wider African research community, the harmonization of data derived from different H3Africa projects, and the promotion of data curation through mapping to ontologies, where applicable. This is to enable data retrieval and comparison and to make the data FAIR

Phenotype Data Collection Standards

In collaboration with the H3Africa Phenotype Harmonisation Working Group, H3ABioNet is establishing common phenotype-specific data collection modules that can be implemented across the African continent (and beyond). These modules incorporate both existing and newly developed phenotype standards, to promote harmonised collection of phenotype data for genomic research. Read more

Other Standards

1. GA4GH Standards

Formed in 2013, the Global Alliance for Genomics and Health (GA4GH) unites an international community dedicated to advancing human health through genomic data. GA4GH builds technical standards, policy frameworks and tools that will expand the responsible, voluntary, and secure use of genomic and other related health data. As a GA4GH driver project, H3ABioNet has been involved in the advancement and implementation of several GA4GH standards including Beacon API, Crypt4GH, DUO, Pedigree, SAM/BAM, VRS, and more. More information about this work can be found in the related publication.

GA4GH: International policies and standards for data sharing across genomic research and healthcare. Rehm et al., (2021)

2. DUO

The Data Use Ontology (DUO) is a GA4GH-developed standard which provides a standard set of terms or consent codes that can be used to tag datasets with use permissions, aiding researchers in discovering data and facilitating DAC decisions in the data access process. The standard allows data to be tagged with consistently defined, computer-readable use permissions and optional modifiers, enables tagged data to be more easily discoverable and accessible, and streamlines the process of identifying appropriate uses and users of data. DUO can be explored via the Ontology Lookup Service. H3ABioNet employs DUO to curate consent for datasets produced in H3Africa. H3ABioNet participated in the evolution of the DUO ontology as well, the publications of which are titled:

Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem. Dyke et al., (2022).
The Data Use Ontology to streamline responsible access to human biomedical datasets. Lawson et al., (2021).

3. GECKO

The Genomic Cohorts Knowledge Ontology (GECKO), developed and maintained by the CINECA project, standardises attributes commonly used for genomics cohort description as well as individual-level data items. The standard enables data to be more easily discoverable and interoperable and can be explored via the Ontology Lookup Service. H3ABioNet employs GECKO to curate cohorts generated in H3Africa. In addition, H3ABioNet/H3Africa served as one of the use cases during GECKO development.

4. PhenX

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org) is a web-based catalogue of recommended measurement protocols of phenotypes and exposures suitable for inclusion in genomic, clinical, and translational research studies with human participants.

The PhenX Toolkit supports consistent data collection by providing detailed protocols for collecting new data via different modes of administration. H3ABioNet has employed PhenX protocols as a reference in the development of the H3Africa Phenotype Data Collection Standards.

Phenotype Harmonization

Ontology Mapping