Browsing by Author "Zass, Lyndon"

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    African Genomic Medicine Portal: A Web Portal for Biomedical Applications
    (2022-02-11) 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
    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.
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    The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research
    (2019-12-30) Kumuthini, Judit; Zass, Lyndon; Panji, Sumir; Salifu, Samson P; Kayondo, Jonathan K; Nembaware, Victoria; Mbiyavanga, Mamana; Olabode, Ajayi; Kishk, Ali; Wells, Gordon; Mulder, Nicola J
    Abstract Background Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)‘s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. Results The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. Conclusion To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.