African Genomic Medicine Portal



Name Description
AGVD The African Genome Variation Database (AGVD) is a platform for exploring genomic variation data within African populations. This project forms part of the H3ABioNet consortium.
AMP A web based portal to collate, curate and provide primary references for African specific microbiome metadata and resources for African based microbiome research.
ClinGen ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinVar ClinVar aggregates information about genomic variation and its relationship to human health.
CPIC The Clinical Pharmacogenetics Implementation Consortium (CPIC®) is an international consortium of individual volunteers and a small dedicated staff who are interested in facilitating the use of pharmacogenetic tests for patient care.
DisGeNET DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases.
Drug Bank The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.
GWAS Catalog The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.
H3Africa Data & Biospecimen Catalogue H3Africa Data and Biospecimen Catalogue was developed for searching H3Africa metadata and samples. The aim of the catalogue is for users to identify datasets, along with their EGA accession numbers and biospecimens, including information on where they are stored. The sets of interest can then be requested via an access request form to the Data and Biospecimens Access Committee.
PharmGKB The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information including clinical guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships.

Tools and Pipelines

Name Description
H3ABioNet Bioinformatics Workflows H3ABioNet developed standard operating procedures (SOPs) for common bioinformatics data analysis tasks. Some SOPs contain a software workflow as well as corresponding containers with all the necessary software dependencies to run the workflow.
HUMA The Human Mutation Analysis (HUMA) database and web server has been developed as a platform for the analysis of genetic variation in humans. HUMA aggregates data from various sources into a single, connected database and provides tools to analyse this data. Further, HUMA provides users with the option of uploading their own variation datasets and using the provided tools to analyse this data.
PharmCAT Pharmacogenomics Clinical Annotation Tool

Online Courses

Name Description
AGMT The purpose of this Professional Development Course is to provide genomics and genetics education to nurses based in Africa. The course will emphasize the practical application of content into learners’ current settings and roles. The problem-based practical sessions will emphasize increased knowledge in the genetics of African health issues. In addition, skills in Genetic counselling, Community engagement/Ethical conduct in research and patient care and development of health promotion material will be reinforced. Therefore the course seeks to support improved Genetics & Genomics knowledge.
IBT The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
16S rRNA Microbiome IntBT The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.
16S rRNA Microbiome IntBT Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential informatics skills required to begin analysing NGS data and apply some of the most commonly used tools and resources for sequence data analysis.