{"doi":"10.1093/nar/gkab1009","title":"AMDB: a database of animal gut microbial communities with manually curated metadata","abstract":"Variations in gut microbiota can be explained by animal host characteristics, including host phylogeny and diet. However, there are currently no databases that allow for easy exploration of the relationship between gut microbiota and diverse animal hosts. The Animal Microbiome Database (AMDB) is the first database to provide taxonomic profiles of the gut microbiota in various animal species. AMDB contains 2530 amplicon data from 34 projects with manually curated metadata. The total data represent 467 animal species and contain 10 478 bacterial taxa. This novel database provides information regarding gut microbiota structures and the distribution of gut bacteria in animals, with an easy-to-use interface. Interactive visualizations are also available, enabling effective investigation of the relationship between the gut microbiota and animal hosts. AMDB will contribute to a better understanding of the gut microbiota of animals. AMDB is publicly available without login requirements at http://leb.snu.ac.kr/amdb.","journal":"Nucleic Acids Research","year":2021,"id":12500,"datarank":1.1726040178488113,"base_score":3.091042453358316,"endowment":3.091042453358316,"self_citation_contribution":0.4636563680037475,"citation_network_contribution":0.7089476498450639,"self_endowment_contribution":0.4636563680037475,"citer_contribution":0.7089476498450639,"corpus_percentile":59.31651749389748,"corpus_rank":501,"citation_count":24,"citer_count":24,"citers_with_citation_signal":20,"citers_with_endowment":20,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9553,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-11-08","fair_score":47.7083,"fair_percentile":44.415127528583994,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":98289,"name":"Jong‐Hyun Park","orcid":"0000-0002-2918-1867","position":1,"is_corresponding":false},{"id":98290,"name":"Yeonjae Jung","orcid":"0000-0002-7022-4152","position":2,"is_corresponding":false},{"id":27571,"name":"Jongsik Chun","orcid":"0000-0003-3385-5171","position":3,"is_corresponding":false},{"id":98288,"name":"Jun-Won Yang","orcid":"0000-0002-9814-6918","position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"34747470","pmcid":"PMC8728277","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":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":0.2259,"fair_rationale":{"fair_score":47.71,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"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":0.5,"signal":null,"rationale":"The paper states that metadata is 'manually curated' and includes host taxonomy and diet, but does not describe machine-readable metadata standards or structured formats."}]},"A":{"name":"Accessible","score":67.5,"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":0.75,"signal":null,"rationale":"The database is freely available at a URL without login, but the paper does not provide a clear protocol for programmatic access or API."}]},"I":{"name":"Interoperable","score":25.0,"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":0.5,"signal":null,"rationale":"The paper uses standard formats like BIOM and CSV, but does not mention use of community-standard vocabularies or persistent identifiers for samples or taxa."}]},"R":{"name":"Reusable","score":33.33,"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":0.5,"signal":null,"rationale":"The data is available under a CC BY license and the paper describes processing steps, but lacks a formal data-availability statement for raw data and does not provide code for reproducibility."}]}},"suggestions":["Provide metadata in a machine-readable format (e.g., JSON-LD or XML) with controlled vocabularies.","Offer a REST API or SPARQL endpoint for programmatic access to the database.","Assign persistent identifiers (e.g., DOIs) to each dataset and sample.","Include a formal data-availability statement that specifies where raw sequencing data and processed files can be accessed.","Publish the analysis code (e.g., QIIME 2 scripts) in a public repository with a license."],"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":"2026-06-18T00:46:29.675261Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}