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African Genomic Medicine Portal: A Web Portal for Biomedical Applications

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 p...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879570/
https://www.ncbi.nlm.nih.gov/pubmed/35207753
http://dx.doi.org/10.3390/jpm12020265
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author 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
author_facet 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
author_sort Othman, Houcemeddine
collection PubMed
description 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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spelling pubmed-88795702022-02-26 African Genomic Medicine Portal: A Web Portal for Biomedical Applications 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 J Pers Med Article 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. MDPI 2022-02-11 /pmc/articles/PMC8879570/ /pubmed/35207753 http://dx.doi.org/10.3390/jpm12020265 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
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
African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title_full African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title_fullStr African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title_full_unstemmed African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title_short African Genomic Medicine Portal: A Web Portal for Biomedical Applications
title_sort african genomic medicine portal: a web portal for biomedical applications
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879570/
https://www.ncbi.nlm.nih.gov/pubmed/35207753
http://dx.doi.org/10.3390/jpm12020265
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