Othman Houcemeddine, Zass Lyndon, da Rocha Jorge E B, Radouani Fouzia, Samtal Chaimae, Benamri Ichrak, Kumuthini Judit, Fakim Yasmina J, Hamdi Yosr, Mezzi Nessrine, Boujemaa Maroua, Okeke Chiamaka Jessica, Tendwa Maureen B, Sanak Kholoud, Chaouch Melek, Panji Sumir, Kefi Rym, Sallam Reem M, Ghoorah Anisah W, Romdhane Lilia, Kiran Anmol, Meintjes Ayton P, Maturure Perceval, Jmel Haifa, Ksouri Ayoub, Azzouzi Maryame, Farahat Mohammed A, Ahmed Samah, Sibira Rania, Turkson Michael E E, Ssekagiri Alfred, Parker Ziyaad, Fadlelmola Faisal M, Ghedira Kais, Mulder Nicola, Kamal Kassim Samar
Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, 9 jubilee Road, Parktown, Johannesburg 2193, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
J Pers Med. 2022 Feb 11;12(2):265. doi: 10.3390/jpm12020265.
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.
目前，基因组学数据正以前所未有的速度产生，这使得知识发现有所增加，并促使更多数据提交至公共数据存储库。尽管取得了这些进展，但与欧洲和亚洲血统人群相比，非洲血统人群的基因组信息仍然非常少。这些信息通常分散在几个不同的生物医学数据存储库中，这些存储库往往缺乏足够的细粒度结构和注释来解释非洲人群的多样性，从而导致了与此类信息的检索、呈现和可发现性相关的诸多挑战。为了克服这些挑战，我们开发了非洲基因组医学门户（AGMP），这是一个包含对非洲血统人群进行的基因组医学研究元数据的数据库。该元数据是从两个与基因组医学相关的公共数据库PharmGKB和DisGeNET中整理而来的。从这些源数据库中检索到的元数据仅限于与非洲血统人群疾病病因或治疗相关的基因组变异。共检索到2000多个与非洲血统人群相关的变异。随后，领域专家整理并注释了与报告这些变异的研究相关的其他信息，包括地理起源、民族语言群体、关联显著水平以及其他相关研究信息，如研究设计和样本量（如有）。AGMP作为一个专门的资源，通过查询变异、基因、疾病和药物，可获取应用于健康研究的非洲特定基因组学信息。该门户及其相应的技术文档、实现代码和内容均可公开获取。
