{"doi":"10.1093/nar/gkab786","title":"gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites","abstract":"gutMGene (http://bio-annotation.cn/gutmgene), a manually curated database, aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. Metagenomic sequencing of fecal samples has identified 3.3 × 106 non-redundant microbial genes from up to 1500 different species. One of the contributions of gut microbiota to host biology is the circulating pool of bacterially derived small-molecule metabolites. It has been estimated that 10% of metabolites found in mammalian blood are derived from the gut microbiota, where they can produce systemic effects on the host through activating or inhibiting gene expression. The current version of gutMGene documents 1331 curated relationships between 332 gut microbes, 207 microbial metabolites and 223 genes in humans, and 2349 curated relationships between 209 gut microbes, 149 microbial metabolites and 544 genes in mice. Each entry in the gutMGene contains detailed information on a relationship between gut microbe, microbial metabolite and target gene, a brief description of the relationship, experiment technology and platform, literature reference and so on. gutMGene provides a user-friendly interface to browse and retrieve each entry using gut microbes, disorders and intervention measures. It also offers the option to download all the entries and submit new experimentally validated associations.","journal":"Nucleic Acids Research","year":2021,"id":1287,"datarank":4.450228368143475,"base_score":5.075173815233827,"endowment":5.075173815233827,"self_citation_contribution":0.7612760722850741,"citation_network_contribution":3.6889522958584005,"self_endowment_contribution":0.7612760722850741,"citer_contribution":3.6889522958584005,"corpus_percentile":70.78925956061839,"corpus_rank":360,"citation_count":167,"citer_count":162,"citers_with_citation_signal":134,"citers_with_endowment":134,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9538,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-09-09","fair_score":52.9167,"fair_percentile":79.11169744942832,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":16292,"name":"Changlu Qi","orcid":null,"position":1,"is_corresponding":false},{"id":16293,"name":"Haixiu Yang","orcid":"0000-0002-7161-1656","position":2,"is_corresponding":false},{"id":16294,"name":"Minke Lu","orcid":null,"position":3,"is_corresponding":false},{"id":16295,"name":"Yiting Cai","orcid":"0000-0001-6295-6989","position":4,"is_corresponding":false},{"id":16296,"name":"Tongze Fu","orcid":null,"position":5,"is_corresponding":false},{"id":16297,"name":"Jialiang Ren","orcid":null,"position":6,"is_corresponding":false},{"id":16298,"name":"Qu Jin","orcid":null,"position":7,"is_corresponding":false},{"id":16299,"name":"Xue Zhang","orcid":"0009-0004-0249-0581","position":8,"is_corresponding":false},{"id":16291,"name":"Liang Cheng","orcid":"0000-0002-6665-6710","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"34500458","pmcid":"PMC8728193","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.697,"fair_rationale":{"fair_score":52.92,"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 describes a database with structured entries (microbe, metabolite, gene, description, methods, references) but does not provide machine-readable metadata (e.g., schema.org, JSON-LD) or mention use of formal metadata standards."}]},"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 accessible at a URL (http://bio-annotation.cn/gutmgene) and allows download of all entries, but the paper does not specify a protocol for programmatic access (e.g., API) or provide a data access statement for the underlying code."}]},"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 database uses standard identifiers (NCBI Taxonomy, PubChem, HMDB, ChEBI, NCBI Gene) and provides data in a downloadable format, but the paper does not specify the use of standard file formats (e.g., CSV, JSON) or controlled vocabularies for relationships."}]},"R":{"name":"Reusable","score":41.67,"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":0.667,"signal":null,"rationale":"The paper includes a data availability statement with a URL for free access, a Creative Commons license (CC BY-NC 4.0), and allows submission of new data, but lacks a formal license for the database itself, no code availability, and no explicit reproducibility details for the curation process."}]}},"suggestions":["Add machine-readable metadata (e.g., JSON-LD or schema.org markup) to the database website to improve findability.","Provide a REST API or SPARQL endpoint for programmatic access to the data.","Specify standard file formats (e.g., CSV, TSV, JSON) for downloads and use controlled vocabularies for relationship types.","Include a clear license for the database content (e.g., CC0 or CC BY) and make the curation code or scripts available in a public repository.","Document the curation protocol in more detail to enable reproducibility, including inclusion/exclusion criteria and quality control steps."],"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":"2026-06-18T00:37:37.908105Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}