{"doi":"10.1093/database/baad092","title":"The African Human Microbiome Portal: a public web portal of curated metagenomic metadata","abstract":"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 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL:  https://microbiome.h3abionet.org/.","journal":"Database","year":2024,"id":11281,"datarank":0.2951630853245002,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.003276562966203134,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.003276562966203134,"corpus_percentile":46.94873881204231,"corpus_rank":653,"citation_count":6,"citer_count":3,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.903,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":61.25,"fair_percentile":92.70008795074759,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":91008,"name":"Mariem Hanachi","orcid":null,"position":1,"is_corresponding":false},{"id":91009,"name":"Nihad Alsayed","orcid":"0000-0002-8462-3277","position":2,"is_corresponding":false},{"id":91010,"name":"Meriem Fassatoui","orcid":null,"position":3,"is_corresponding":false},{"id":91011,"name":"Ovokeraye H. Oduaran","orcid":"0000-0002-3033-7873","position":4,"is_corresponding":false},{"id":91012,"name":"Imane Allali","orcid":"0000-0002-7662-5643","position":5,"is_corresponding":false},{"id":91013,"name":"Suresh Maslamoney","orcid":"0000-0002-3118-8945","position":6,"is_corresponding":false},{"id":12775,"name":"Ayton Meintjes","orcid":"0000-0001-5076-2941","position":7,"is_corresponding":false},{"id":91014,"name":"Lyndon Zass","orcid":"0000-0001-8862-1706","position":8,"is_corresponding":false},{"id":91015,"name":"Jorge Da Rocha","orcid":null,"position":9,"is_corresponding":false},{"id":91016,"name":"Rym Kefi","orcid":null,"position":10,"is_corresponding":false},{"id":1678,"name":"Alia Benkahla","orcid":"0000-0001-9988-3250","position":11,"is_corresponding":false},{"id":91017,"name":"Kais Ghedira","orcid":null,"position":12,"is_corresponding":false},{"id":91018,"name":"Sumir Panji","orcid":"0000-0003-0447-0598","position":13,"is_corresponding":false},{"id":62302,"name":"Nicola Mulder","orcid":"0000-0003-4905-0941","position":14,"is_corresponding":false},{"id":91019,"name":"Faisal M. Fadlelmola","orcid":"0000-0001-8351-264X","position":15,"is_corresponding":false},{"id":1674,"name":"Oussema Souiai","orcid":null,"position":16,"is_corresponding":false},{"id":91020,"name":"Rym Kéfi","orcid":"0000-0001-8801-5781","position":17,"is_corresponding":false},{"id":91021,"name":"Kaïs Ghedira","orcid":"0000-0002-3387-6493","position":18,"is_corresponding":false},{"id":86415,"name":"Anmol Kiran","orcid":"0000-0003-2680-2303","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38204360","pmcid":"PMC10782148","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":77.5,"fair_a":80.0,"fair_i":37.5,"fair_r":50.0,"fair_zscore":1.4508,"fair_rationale":{"fair_score":61.25,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The paper describes rich, curated metadata with ontology terms (Disease Ontology, AfPO) and a predefined guideline, but does not provide machine-readable metadata (e.g., JSON-LD, RDF) or explicit FAIR metadata standards."}]},"A":{"name":"Accessible","score":80.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"The portal is openly accessible at a clear URL (https://microbiome.h3abionet.org/) with download options, and the source code is available under GPLv3, but no explicit authentication/authorization protocol is mentioned."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The paper uses standard formats (CSV, SQLite), ontologies (Disease Ontology, AfPO), and references MIMS/FAIR, but does not fully adopt community-standard vocabularies or persistent identifiers for all metadata fields."}]},"R":{"name":"Reusable","score":50.0,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.833,"signal":null,"rationale":"The paper provides a clear data-availability statement (URL, open access), a license (CC BY 4.0), and code (GPLv3), but lacks explicit reproducibility instructions or a formal data citation for the curated metadata."}]}},"suggestions":["Publish the curated metadata in a machine-readable format (e.g., JSON-LD or RDF) with FAIR-compliant metadata schemas.","Assign persistent identifiers (e.g., DOIs) to the curated metadata and each bioproject record for better findability.","Provide a formal data citation and versioning for the portal's dataset to enhance reusability.","Include explicit documentation on how to reproduce the curation pipeline (e.g., a reproducible workflow with containerized scripts).","Adopt community-standard ontologies (e.g., MIMS, MIxS) for all metadata fields and ensure consistent use of controlled vocabularies."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:52:16.878317Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}