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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-8879570 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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