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Abstract
Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.
Highlights
Modern biomedical research is strongly reliant on data repositories that are wellstructured for the storage and retrieval of information
The portal was developed to provide curated information on the genetic variations associated with disease aetiology and treatment in populations of African-ancestry as well as a broad overview of the disease-causing/-associated variants
The African Genomic Medicine Portal (AGMP) is a user-friendly resource that allows users to query curated African genomic variants linked to either clinical phenotypes or to drug response using gene, disease, variant and drug names. This portal should be of interest to the African scientific community, physicians and genomic medicine stakeholders worldwide, as it provides informative data for those working with individuals of African descent
Summary
Modern biomedical research is strongly reliant on data repositories that are wellstructured for the storage and retrieval of information. The number of biological and biomedical databases have increased over the last two decades, with resources for diverse organisms, molecules, interactions and pathways. The goal of research is often compounded by the complexity of these different sources and the amount of data that are being gathered from high-throughput technologies, which has increased in the past two decades. Low- and middle-income regions, such as Africa, are still not fully capable of tapping into genomic resources for biomedical application due to unmatched resources and needs. There is an urgent need to improve facilities, for data generation, processing, storage and access, that will contribute to the implementation of genomic medicine in Africa. Recent initiatives have begun to enhance efforts to overcome the barriers for the use of genomics in Africa, including the Malaria Genomic Epidemiology Network (MalariaGEN) and the Human Heredity and Health in Africa (H3Africa) consortium [1]
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