{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T15:37:24Z","timestamp":1766504244232,"version":"3.41.2"},"reference-count":41,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T00:00:00Z","timestamp":1704844800000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The National Human Genome Research Institute of the National Institutes of Health","award":["H3ABioNet U24HG006941"],"award-info":[{"award-number":["H3ABioNet U24HG006941"]}]},{"name":"The National Human Genome Research Institute of the National Institutes of Health","award":["H3ABioNet U24HG006941"],"award-info":[{"award-number":["H3ABioNet U24HG006941"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https:\/\/microbiome.h3abionet.org\/. This web portal is open access and offers an interactive visualization of 14\u2009889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user\u2019s applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome.<\/jats:p>\n               <jats:p>Database URL: \u00a0https:\/\/microbiome.h3abionet.org\/.<\/jats:p>","DOI":"10.1093\/database\/baad092","type":"journal-article","created":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T19:21:57Z","timestamp":1704914517000},"source":"Crossref","is-referenced-by-count":6,"title":["The African Human Microbiome Portal: a public web portal of curated metagenomic metadata"],"prefix":"10.1093","volume":"2024","author":[{"given":"Anmol","family":"Kiran","sequence":"first","affiliation":[]},{"given":"Mariem","family":"Hanachi","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar , Tunis 1002, Tunisia"},{"name":"Faculty of Science of Bizerte, University of Carthage , Tunis, Tunisia"}]},{"given":"Nihad","family":"Alsayed","sequence":"additional","affiliation":[{"name":"Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization , Khartoum, Sudan"}]},{"given":"Meriem","family":"Fassatoui","sequence":"additional","affiliation":[{"name":"Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar , Tunis 1002, Tunisia"}]},{"given":"Ovokeraye H","family":"Oduaran","sequence":"additional","affiliation":[{"name":"The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa"}]},{"given":"Imane","family":"Allali","sequence":"additional","affiliation":[{"name":"Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat , Rabat, Morocco"}]},{"given":"Suresh","family":"Maslamoney","sequence":"additional","affiliation":[{"name":"Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town 7925, South Africa"}]},{"given":"Ayton","family":"Meintjes","sequence":"additional","affiliation":[{"name":"Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town 7925, South Africa"}]},{"given":"Lyndon","family":"Zass","sequence":"additional","affiliation":[{"name":"Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town 7925, South Africa"}]},{"given":"Jorge Da","family":"Rocha","sequence":"additional","affiliation":[{"name":"The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa"}]},{"given":"Rym","family":"Kefi","sequence":"additional","affiliation":[{"name":"Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar , Tunis 1002, Tunisia"}]},{"given":"Alia","family":"Benkahla","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar , Tunis 1002, Tunisia"}]},{"given":"Kais","family":"Ghedira","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar , Tunis 1002, Tunisia"}]},{"given":"Sumir","family":"Panji","sequence":"additional","affiliation":[{"name":"Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town 7925, South Africa"}]},{"given":"Nicola","family":"Mulder","sequence":"additional","affiliation":[{"name":"Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town 7925, South Africa"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8351-264X","authenticated-orcid":false,"given":"Faisal M","family":"Fadlelmola","sequence":"additional","affiliation":[{"name":"Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization , Khartoum, Sudan"}]},{"given":"Oussema","family":"Souiai","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar , Tunis 1002, Tunisia"},{"name":"Malawi-Liverpool-Wellcome Trust , Blantyre 3, Malawi"},{"name":"Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool CH64 7TE, UK"}]}],"member":"286","published-online":{"date-parts":[[2024,1,10]]},"reference":[{"key":"2024062912171702900_R1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00394-018-1703-4","article-title":"The role of the microbiome for human health: from basic science to clinical applications","volume":"57","author":"Mohajeri","year":"2018","journal-title":"Eur. J. Nutr."},{"key":"2024062912171702900_R2","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1097\/MOG.0000000000000139","article-title":"The gut microbiome in health and in disease","volume":"31","author":"Shreiner","year":"2015","journal-title":"Curr. Opin. Gastroenterol."},{"key":"2024062912171702900_R3","doi-asserted-by":"crossref","first-page":"D15","DOI":"10.1093\/nar\/gkq1150","article-title":"The International Nucleotide Sequence Database Collaboration","volume":"39","author":"Cochrane","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R4","doi-asserted-by":"crossref","first-page":"D28","DOI":"10.1093\/nar\/gkq967","article-title":"The European Nucleotide Archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R5","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R6","doi-asserted-by":"crossref","first-page":"D25","DOI":"10.1093\/nar\/gkw1001","article-title":"DNA Data Bank of Japan","volume":"45","author":"Mashima","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/978-1-4939-3369-3_13","article-title":"MG-RAST, a metagenomics service for analysis of microbial community structure and function","volume":"1399","author":"Keegan","year":"2016","journal-title":"Methods Mol. Biol. Clifton. NJ"},{"key":"2024062912171702900_R8","doi-asserted-by":"crossref","first-page":"D123","DOI":"10.1093\/nar\/gkr975","article-title":"IMG\/M: the integrated metagenome data management and comparative analysis system","volume":"40","author":"Markowitz","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R9","doi-asserted-by":"crossref","first-page":"D600","DOI":"10.1093\/nar\/gkt961","article-title":"EBI metagenomics\u2014a new resource for the analysis and archiving of metagenomic data","volume":"42","author":"Hunter","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R10","first-page":"D570","article-title":"MGnify: the microbiome analysis resource in 2020","volume":"48","author":"Mitchell","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R11","doi-asserted-by":"crossref","first-page":"D637","DOI":"10.1093\/nar\/gky1008","article-title":"gcMeta: a global catalogue of metagenomics platform to support the archiving, standardization and analysis of microbiome data","volume":"47","author":"Shi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R12","doi-asserted-by":"crossref","first-page":"D692","DOI":"10.1093\/nar\/gkx1036","article-title":"The MAR databases: development and implementation of databases specific for marine metagenomics","volume":"46","author":"Klemetsen","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R13","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1111\/1758-2229.12686","article-title":"Coral microbiome database: integration of sequences reveals high diversity and relatedness of coral-associated microbes","volume":"11","author":"Huggett","year":"2019","journal-title":"Environ. Microbiol. Rep."},{"key":"2024062912171702900_R14","first-page":"D626","article-title":"TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes","volume":"48","author":"Corr\u00eaa","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R15","article-title":"The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information","volume":"2010","author":"Chen","year":"2010","journal-title":"Database J. Biol. Databases Curation"},{"key":"2024062912171702900_R16","article-title":"SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata","volume":"2022","author":"Agostinetto","year":"2022","journal-title":"Database J. Biol. Databases Curation"},{"key":"2024062912171702900_R17","doi-asserted-by":"crossref","first-page":"D604","DOI":"10.1093\/nar\/gkv1216","article-title":"HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes","volume":"44","author":"Forster","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R18","doi-asserted-by":"crossref","first-page":"D554","DOI":"10.1093\/nar\/gkz843","article-title":"gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions","volume":"48","author":"Cheng","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R19","doi-asserted-by":"crossref","DOI":"10.1186\/s12866-018-1197-5","article-title":"Disbiome database: linking the microbiome to disease","volume":"18","author":"Janssens","year":"2018","journal-title":"BMC Microbiol."},{"key":"2024062912171702900_R20","doi-asserted-by":"crossref","first-page":"D777","DOI":"10.1093\/nar\/gkab1019","article-title":"GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison","volume":"50","author":"Dai","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R21","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkz764","article-title":"GMrepo: a database of curated and consistently annotated human gut metagenomes","volume":"48","author":"Wu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R22","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gkab973","article-title":"mBodyMap: a curated database for microbes across human body and their associations with health and diseases","volume":"50","author":"Jin","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R23","doi-asserted-by":"crossref","first-page":"D729","DOI":"10.1093\/nar\/gkab1009","article-title":"AMDB: a database of animal gut microbial communities with manually curated metadata","volume":"50","author":"Yang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R24","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nbt1360","article-title":"The minimum information about a genome sequence (MIGS) specification","volume":"26","author":"Field","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2024062912171702900_R25","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2024062912171702900_R26","doi-asserted-by":"crossref","DOI":"10.1186\/s40793-022-00425-1","article-title":"Metadata harmonization\u2013standards are the key for a better usage of omics data for integrative microbiome analysis","volume":"17","author":"Cernava","year":"2022","journal-title":"Environ. Microbio."},{"key":"2024062912171702900_R27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2002925","article-title":"The Genomic Observatories Metadatabase (GeOMe): a new repository for field and sampling event metadata associated with genetic samples","volume":"15","author":"Deck","year":"2017","journal-title":"PLoS Biol."},{"key":"2024062912171702900_R28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-020-01204-9","article-title":"The archives are half-empty: an assessment of the availability of microbial community sequencing data","volume":"3","author":"Jurburg","year":"2020","journal-title":"Commun. Biol."},{"key":"2024062912171702900_R29","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1093\/bioinformatics\/btx334","article-title":"MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive","volume":"33","author":"Bernstein","year":"2017","journal-title":"Bioinforma. Oxf. Engl."},{"key":"2024062912171702900_R30","doi-asserted-by":"crossref","DOI":"10.1016\/j.tim.2019.05.006","article-title":"Surveying gut microbiome research in Africans: toward improved diversity and representation","volume":"27","author":"Brewster","year":"2019","journal-title":"Trends Microbiol."},{"key":"2024062912171702900_R31","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1089\/omi.2021.0004","article-title":"Human OMICs and computational biology research in Africa: current challenges and prospects","volume":"25","author":"Hamdi","year":"2021","journal-title":"Omics J. Integr. Biol."},{"key":"2024062912171702900_R32","doi-asserted-by":"crossref","first-page":"R166","DOI":"10.1016\/j.cub.2009.11.050","article-title":"The evolution of human genetic and phenotypic variation in Africa","volume":"20","author":"Campbell","year":"2010","journal-title":"Curr. Biol. CB"},{"key":"2024062912171702900_R33","first-page":"D45","article-title":"DDBJ Database updates and computational infrastructure enhancement","volume":"48","author":"Ogasawara","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R34","doi-asserted-by":"crossref","first-page":"D955","DOI":"10.1093\/nar\/gky1032","article-title":"Human Disease Ontology 2018 update: classification, content and workflow expansion","volume":"47","author":"Schriml","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3001536","article-title":"Public human microbiome data are dominated by highly developed countries","volume":"20","author":"Abdill","year":"2022","journal-title":"PLoS Biol."},{"key":"2024062912171702900_R36","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01194\u201320","article-title":"Microbiome metadata standards: report of the National Microbiome Data Collaborative\u2019s workshop and follow-on activities","volume":"6","author":"Vangay","year":"2021","journal-title":"mSystems"},{"key":"2024062912171702900_R37","doi-asserted-by":"crossref","first-page":"D743","DOI":"10.1093\/nar\/gkaa1031","article-title":"HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes","volume":"49","author":"Kasmanas","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024062912171702900_R38","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2024062912171702900_R39","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-020-03694-0","article-title":"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI\u2019s sequence read archive","volume":"21","author":"Qui\u00f1ones","year":"2020","journal-title":"BMC Bioinf."},{"key":"2024062912171702900_R40","doi-asserted-by":"crossref","DOI":"10.1101\/2021.05.05.442781","article-title":"Current challenges in microbiome metadata collection","author":"Rosenfeld","year":"2021"},{"key":"2024062912171702900_R41","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-021-01195-7","article-title":"Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research","volume":"9","author":"Allali","year":"2021","journal-title":"Microbiome"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad092\/58365397\/baad092.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad092\/58365397\/baad092.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T12:23:25Z","timestamp":1719663805000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad092\/7514669"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,1]]},"references-count":41,"URL":"https:\/\/doi.org\/10.1093\/database\/baad092","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2024,1,1]]},"published":{"date-parts":[[2024,1,1]]},"article-number":"baad092"}}