African Genomic Medicine Portal: A Web Portal for Biomedical Applications

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dc.contributor.authorOthman, Houcemeddine
dc.contributor.authorZass, Lyndon
dc.contributor.authorda Rocha, Jorge E B
dc.contributor.authorRadouani, Fouzia
dc.contributor.authorSamtal, Chaimae
dc.contributor.authorBenamri, Ichrak
dc.contributor.authorKumuthini, Judit
dc.contributor.authorFakim, Yasmina J
dc.contributor.authorHamdi, Yosr
dc.contributor.authorMezzi, Nessrine
dc.contributor.authorBoujemaa, Maroua
dc.contributor.authorOkeke, Chiamaka Jessica
dc.contributor.authorTendwa, Maureen B
dc.contributor.authorSanak, Kholoud
dc.contributor.authorChaouch, Melek
dc.contributor.authorPanji, Sumir
dc.contributor.authorKefi, Rym
dc.contributor.authorSallam, Reem M
dc.contributor.authorGhoorah, Anisah W
dc.contributor.authorRomdhane, Lilia
dc.contributor.authorKiran, Anmol
dc.contributor.authorMeintjes, Ayton P
dc.contributor.authorMaturure, Perceval
dc.contributor.authorJmel, Haifa
dc.contributor.authorKsouri, Ayoub
dc.contributor.authorAzzouzi, Maryame
dc.contributor.authorFarahat, Mohammed A
dc.contributor.authorAhmed, Samah
dc.contributor.authorSibira, Rania
dc.contributor.authorTurkson, Michael E E
dc.contributor.authorSsekagiri, Alfred
dc.contributor.authorParker, Ziyaad
dc.contributor.authorFadlelmola, Faisal M
dc.contributor.authorGhedira, Kais
dc.contributor.authorMulder, Nicola
dc.contributor.authorKamal Kassim, Samar
dc.date.accessioned2022-04-09T16:42:27Z
dc.date.available2022-04-09T16:42:27Z
dc.date.issued2022-02-11
dc.date.updated2022-02-24T14:50:13Z
dc.description.abstractGenomics 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.en_US
dc.identifierdoi: 10.3390/jpm12020265
dc.identifier.apacitationOthman, H., Zass, L., da Rocha, J. E. B., Radouani, F., Samtal, C., Benamri, I., ... Kamal Kassim, S. (2022). African Genomic Medicine Portal: A Web Portal for Biomedical Applications. <i>Journal of Personalized Medicine</i>, 12(2), 265. http://hdl.handle.net/11427/36317en_ZA
dc.identifier.chicagocitationOthman, Houcemeddine, Lyndon Zass, Jorge E B da Rocha, Fouzia Radouani, Chaimae Samtal, Ichrak Benamri, Judit Kumuthini, et al "African Genomic Medicine Portal: A Web Portal for Biomedical Applications." <i>Journal of Personalized Medicine</i> 12, 2. (2022): 265. http://hdl.handle.net/11427/36317en_ZA
dc.identifier.citationOthman, H., Zass, L., da Rocha, J.E.B., Radouani, F., Samtal, C., Benamri, I., Kumuthini, J. & Fakim, Y.J. et al. 2022. African Genomic Medicine Portal: A Web Portal for Biomedical Applications. <i>Journal of Personalized Medicine.</i> 12(2):265. http://hdl.handle.net/11427/36317en_ZA
dc.identifier.ris TY - Journal Article AU - Othman, Houcemeddine AU - Zass, Lyndon AU - da Rocha, Jorge E B AU - Radouani, Fouzia AU - Samtal, Chaimae AU - Benamri, Ichrak AU - Kumuthini, Judit AU - Fakim, Yasmina J AU - Hamdi, Yosr AU - Mezzi, Nessrine AU - Boujemaa, Maroua AU - Okeke, Chiamaka Jessica AU - Tendwa, Maureen B AU - Sanak, Kholoud AU - Chaouch, Melek AU - Panji, Sumir AU - Kefi, Rym AU - Sallam, Reem M AU - Ghoorah, Anisah W AU - Romdhane, Lilia AU - Kiran, Anmol AU - Meintjes, Ayton P AU - Maturure, Perceval AU - Jmel, Haifa AU - Ksouri, Ayoub AU - Azzouzi, Maryame AU - Farahat, Mohammed A AU - Ahmed, Samah AU - Sibira, Rania AU - Turkson, Michael E E AU - Ssekagiri, Alfred AU - Parker, Ziyaad AU - Fadlelmola, Faisal M AU - Ghedira, Kais AU - Mulder, Nicola AU - Kamal Kassim, Samar AB - 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. DA - 2022-02-11 DB - OpenUCT DP - University of Cape Town IS - 2 J1 - Journal of Personalized Medicine LK - https://open.uct.ac.za PY - 2022 T1 - African Genomic Medicine Portal: A Web Portal for Biomedical Applications TI - African Genomic Medicine Portal: A Web Portal for Biomedical Applications UR - http://hdl.handle.net/11427/36317 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/36317
dc.identifier.vancouvercitationOthman H, Zass L, da Rocha JEB, Radouani F, Samtal C, Benamri I, et al. African Genomic Medicine Portal: A Web Portal for Biomedical Applications. Journal of Personalized Medicine. 2022;12(2):265. http://hdl.handle.net/11427/36317.en_ZA
dc.language.isoenen_US
dc.publisher.departmentComputational Biology Divisionen_US
dc.publisher.facultyFaculty of Health Sciencesen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceJournal of Personalized Medicineen_US
dc.source.journalissue2en_US
dc.source.journalvolume12en_US
dc.source.pagination265en_US
dc.source.urihttps://www.mdpi.com/journal/jpm
dc.titleAfrican Genomic Medicine Portal: A Web Portal for Biomedical Applicationsen_US
dc.typeJournal Articleen_US
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