{"doi":"10.1093/nar/gkac1049","title":"MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters","abstract":"With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.","journal":"Nucleic Acids Research","year":2022,"id":231767,"datarank":3.776699216143421,"base_score":6.135564891081739,"endowment":6.135564891081739,"self_citation_contribution":0.9203347336622609,"citation_network_contribution":2.8563644824811605,"self_endowment_contribution":0.9203347336622609,"citer_contribution":2.8563644824811605,"corpus_percentile":94.05894639127408,"corpus_rank":769,"citation_count":461,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.934,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":39.5833,"fair_percentile":53.53103026597371,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":839412,"name":"Kai Blin","orcid":"0000-0003-3764-6051","position":1,"is_corresponding":false},{"id":839413,"name":"Jorge C. Navarro-Muñoz","orcid":"0000-0003-2992-1607","position":2,"is_corresponding":false},{"id":413184,"name":"Nicole E. Avalon","orcid":"0000-0003-3588-892X","position":3,"is_corresponding":false},{"id":63491,"name":"Marc G. Chevrette","orcid":"0000-0002-7209-0717","position":4,"is_corresponding":false},{"id":839414,"name":"Susan Egbert","orcid":"0000-0001-5458-1099","position":5,"is_corresponding":false},{"id":839415,"name":"Sang Hyeon Lee","orcid":"0000-0002-1377-3913","position":6,"is_corresponding":false},{"id":839416,"name":"David Meijer","orcid":"0000-0001-6406-4394","position":7,"is_corresponding":false},{"id":839417,"name":"Michael J. J. Recchia","orcid":"0000-0002-1450-0941","position":8,"is_corresponding":false},{"id":839418,"name":"Zachary L. Reitz","orcid":"0000-0003-1964-8221","position":9,"is_corresponding":false},{"id":295894,"name":"Jeffrey A. van Santen","orcid":"0000-0002-5424-804X","position":10,"is_corresponding":false},{"id":839419,"name":"Nelly Sélem‐Mójica","orcid":"0000-0003-1697-3862","position":11,"is_corresponding":false},{"id":839420,"name":"Thomas Tørring","orcid":"0000-0001-5257-2121","position":12,"is_corresponding":false},{"id":839421,"name":"Liana Zaroubi","orcid":"0000-0001-8218-7216","position":13,"is_corresponding":false},{"id":839422,"name":"Mohammad Alanjary","orcid":"0000-0001-8420-1325","position":14,"is_corresponding":false},{"id":262563,"name":"Gajender Aleti","orcid":"0000-0002-1867-9758","position":15,"is_corresponding":false},{"id":839423,"name":"César Aguilar","orcid":"0000-0001-7044-2419","position":16,"is_corresponding":false},{"id":839424,"name":"Suhad A. A. Al-Salihi","orcid":"0000-0001-7665-7904","position":17,"is_corresponding":false},{"id":806324,"name":"Hannah E. Augustijn","orcid":"0000-0002-1862-6699","position":18,"is_corresponding":false},{"id":839425,"name":"J. Abraham Avelar‐Rivas","orcid":"0000-0003-4216-3556","position":19,"is_corresponding":false},{"id":839426,"name":"Luis Alfredo Avitia-Dominguez","orcid":"0000-0002-5902-2410","position":20,"is_corresponding":false},{"id":839427,"name":"Francisco Barona‐Gómez","orcid":"0000-0003-1492-9497","position":21,"is_corresponding":false},{"id":839428,"name":"Jordan Bernaldo-Agüero","orcid":"0000-0002-7753-5527","position":22,"is_corresponding":false},{"id":308432,"name":"Vincent A. Bielinski","orcid":"0000-0002-8107-8752","position":23,"is_corresponding":false},{"id":839429,"name":"Friederike Biermann","orcid":"0000-0002-9152-2562","position":24,"is_corresponding":false},{"id":839430,"name":"Thomas Booth","orcid":"0000-0002-6134-1488","position":25,"is_corresponding":false},{"id":630663,"name":"Víctor J. Carrión","orcid":"0000-0002-4093-0355","position":26,"is_corresponding":false},{"id":630664,"name":"Raquel Castelo‐Branco","orcid":"0000-0001-6627-0140","position":27,"is_corresponding":false},{"id":839431,"name":"Fernanda O. Chagas","orcid":"0000-0001-9534-3521","position":28,"is_corresponding":false},{"id":416290,"name":"Pablo Cruz‐Morales","orcid":"0000-0002-6751-8897","position":29,"is_corresponding":false},{"id":630668,"name":"Chao Du","orcid":"0000-0003-3447-5293","position":30,"is_corresponding":false},{"id":242697,"name":"Katherine Duncan","orcid":"0000-0002-3670-4849","position":31,"is_corresponding":false},{"id":839432,"name":"Athina Gavriilidou","orcid":"0000-0002-6805-3868","position":32,"is_corresponding":false},{"id":839433,"name":"Damien Gayrard","orcid":"0000-0002-1447-9548","position":33,"is_corresponding":false},{"id":839434,"name":"Karina Gutiérrez-García","orcid":"0000-0002-6077-7490","position":34,"is_corresponding":false},{"id":570814,"name":"Kristina Haslinger","orcid":"0000-0003-1361-1508","position":35,"is_corresponding":false},{"id":261991,"name":"Eric J. N. Helfrich","orcid":"0000-0001-8751-3279","position":36,"is_corresponding":false},{"id":105888,"name":"Justin J. J. van der Hooft","orcid":"0000-0002-9340-5511","position":37,"is_corresponding":false},{"id":839435,"name":"AFIF PRANAYA JATI","orcid":"0000-0002-3147-6293","position":38,"is_corresponding":false},{"id":379253,"name":"Edward Kalkreuter","orcid":"0000-0002-8241-4455","position":39,"is_corresponding":false},{"id":839436,"name":"Nikolaos Kalyvas","orcid":"0000-0002-5676-1859","position":40,"is_corresponding":false},{"id":105865,"name":"Kyo Bin Kang","orcid":"0000-0003-3290-1017","position":41,"is_corresponding":false},{"id":295895,"name":"Satria A. Kautsar","orcid":"0000-0002-9815-511X","position":42,"is_corresponding":false},{"id":839437,"name":"Wonyong Kim","orcid":"0000-0002-9094-8908","position":43,"is_corresponding":false},{"id":702557,"name":"Aditya M. Kunjapur","orcid":"0000-0001-6869-9530","position":44,"is_corresponding":false},{"id":300655,"name":"Yong‐Xin Li","orcid":"0000-0003-4422-2302","position":45,"is_corresponding":false},{"id":839438,"name":"Geng-Min Lin","orcid":"0000-0001-8123-0921","position":46,"is_corresponding":false},{"id":839439,"name":"Catarina Loureiro","orcid":"0000-0002-6258-2080","position":47,"is_corresponding":false},{"id":811553,"name":"Joris J. R. Louwen","orcid":"0000-0003-4887-9109","position":48,"is_corresponding":false},{"id":839440,"name":"Nico L L Louwen","orcid":"0000-0002-4431-5499","position":49,"is_corresponding":false},{"id":651859,"name":"George Lund","orcid":"0000-0001-9099-3461","position":50,"is_corresponding":false},{"id":618635,"name":"Jonathan Parra","orcid":"0000-0001-7273-0406","position":51,"is_corresponding":false},{"id":625834,"name":"Benjamin Philmus","orcid":"0000-0003-2085-0873","position":52,"is_corresponding":false},{"id":839441,"name":"Bita Pourmohsenin","orcid":"0000-0002-5754-7221","position":53,"is_corresponding":false},{"id":809963,"name":"Lotte J. U. Pronk","orcid":"0000-0002-3083-954X","position":54,"is_corresponding":false},{"id":839442,"name":"Adriana Rego","orcid":"0000-0001-9647-1197","position":55,"is_corresponding":false},{"id":839443,"name":"Rex Devasahayam Arokia Balaya","orcid":"0000-0002-9556-3150","position":56,"is_corresponding":false},{"id":381314,"name":"Serina L. Robinson","orcid":"0000-0001-6947-7913","position":57,"is_corresponding":false},{"id":839444,"name":"Luis Rodrigo Rosas-Becerra","orcid":"0000-0002-4105-1563","position":58,"is_corresponding":false},{"id":839445,"name":"Eve Tallulah Roxborough","orcid":"0000-0002-4573-1670","position":59,"is_corresponding":false},{"id":630652,"name":"Michelle Schorn","orcid":"0000-0001-8144-6052","position":60,"is_corresponding":false},{"id":839446,"name":"Darren Scobie","orcid":"0000-0002-9858-9444","position":61,"is_corresponding":false},{"id":839447,"name":"Kumar Saurabh Singh","orcid":"0000-0001-8352-5897","position":62,"is_corresponding":false},{"id":839448,"name":"Nika Sokolova","orcid":"0000-0003-4129-2890","position":63,"is_corresponding":false},{"id":726847,"name":"Xiaoyu Tang","orcid":"0000-0002-7855-5984","position":64,"is_corresponding":false},{"id":839449,"name":"Daniel Udwary","orcid":"0000-0002-3491-0198","position":65,"is_corresponding":false},{"id":840756,"name":"Aruna Vigneshwari","orcid":null,"position":66,"is_corresponding":false},{"id":839450,"name":"Kristiina Vind","orcid":"0000-0001-6307-1461","position":67,"is_corresponding":false},{"id":756335,"name":"Sophie P. J. M. Vromans","orcid":"0000-0002-7482-5721","position":68,"is_corresponding":false},{"id":839451,"name":"Valentin Waschulin","orcid":"0000-0002-8905-1263","position":69,"is_corresponding":false},{"id":839452,"name":"Sam E. Williams","orcid":"0000-0002-6949-426X","position":70,"is_corresponding":false},{"id":312362,"name":"Jaclyn M. Winter","orcid":"0000-0001-6273-5377","position":71,"is_corresponding":false},{"id":839453,"name":"Thomas E. Witte","orcid":"0000-0002-6385-3655","position":72,"is_corresponding":false},{"id":839454,"name":"Huali Xie","orcid":"0000-0002-6581-9573","position":73,"is_corresponding":false},{"id":753410,"name":"Dong Yang","orcid":"0000-0003-2917-0663","position":74,"is_corresponding":false},{"id":839455,"name":"Jingwei Yu","orcid":"0000-0003-4268-436X","position":75,"is_corresponding":false},{"id":585411,"name":"Mitja M. Zdouc","orcid":"0000-0001-6534-6609","position":76,"is_corresponding":false},{"id":300652,"name":"Zheng Zhong","orcid":"0000-0002-1262-4115","position":77,"is_corresponding":false},{"id":839456,"name":"Jérôme Collemare","orcid":"0000-0001-8152-6642","position":78,"is_corresponding":false},{"id":261980,"name":"Roger G. Linington","orcid":"0000-0003-1818-4971","position":79,"is_corresponding":false},{"id":839457,"name":"Tilmann Weber","orcid":"0000-0002-8260-5120","position":80,"is_corresponding":false},{"id":36673,"name":"Marnix H. Medema","orcid":"0000-0002-2191-2821","position":81,"is_corresponding":false},{"id":839411,"name":"Barbara R. Terlouw","orcid":"0000-0002-4058-6718","position":0,"is_corresponding":true}],"reference_count":26,"raw_metadata":null,"created_at":"2026-07-19T00:20:51.245255Z","pmid":"36399496","pmcid":"PMC9825592","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":55.5556,"fair_a":37.5,"fair_i":60.0,"fair_r":45.8333,"fair_zscore":0.2032,"fair_rationale":{"fair_score":39.58,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":55.56,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.","grounded":true,"rationale":"The paper provides a web URL for the data, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","grounded":false,"rationale":"The paper names 'MIBiG Repository' as the holder, which is a domain-specific repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","grounded":false,"rationale":"The data availability statement points to a repository with a URL, which is a public repository link (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Table 2. Entries in MIBiG 3.0 by phylum","grounded":true,"rationale":"The paper contains a table (Table 2) that itemises the number of entries per phylum, which is an inventory of the dataset. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","grounded":false,"rationale":"The dataset identifier (the URL) appears only in the body text of the Data Availability section, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":37.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"There is no access restriction for academic or commercial use of the repository and its data.","grounded":false,"rationale":"The text gives a route to the data with no stated precondition, stating the data are freely available. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"There is no access restriction for academic or commercial use of the repository and its data.","grounded":false,"rationale":"The text explicitly states 'no access restriction', which is a synonym for open access, so an access-level label is present. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive human-subject data and no gatekeeper is named in the text.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not mention any retention period, persistence commitment, or availability timing for the data.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All data can be easily downloaded and parsed in bulk from our database in JSON and GenBank format","grounded":false,"rationale":"JSON and GenBank are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format","grounded":true,"rationale":"The MIBiG standard is a community standard for BGC annotation. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for an external resource (e.g., database accession, RRID) is given in the text. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":45.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name a standard open license for the data; it only states that there is no access restriction, which is not a named license.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"PIKAChU (20)","grounded":true,"rationale":"The paper names PIKAChU as a software tool used for SMILES validation during data production. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The source code components, JSON-formatted data standard, and SQL schema for the MIBiG Repository are available on GitHub","grounded":false,"rationale":"A JSON schema and SQL schema are named as documentation objects that travel with the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"MIBiG 3.0","grounded":false,"rationale":"The paper consistently uses 'MIBiG 3.0' as a version token for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The source code components, JSON-formatted data standard, and SQL schema for the MIBiG Repository are available on GitHub (https://github.com/mibig-secmet)","grounded":false,"rationale":"A machine-resolvable GitHub URL is given for the code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"948770-DECIPHER","grounded":true,"rationale":"The paper lists an ERC Starting Grant number (948770-DECIPHER) among other award numbers.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name a standard open license for the data; it only states that there is no access restriction, which is not a named license.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.","why":"The paper provides a web URL for the data, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","why":"The paper names 'MIBiG Repository' as the holder, which is a domain-specific repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"There is no access restriction for academic or commercial use of the repository and its data.","why":"The text gives a route to the data with no stated precondition, stating the data are freely available. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","why":"The dataset identifier (the URL) appears only in the body text of the Data Availability section, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open neuroimaging formats such as NIfTI or BIDS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data can be easily downloaded and parsed in bulk from our database in JSON and GenBank format","why":"JSON and GenBank are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The source code components, JSON-formatted data standard, and SQL schema for the MIBiG Repository are available on GitHub (https://github.com/mibig-secmet)","why":"A machine-resolvable GitHub URL is given for the code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"MIBiG 3.0","why":"The paper consistently uses 'MIBiG 3.0' as a version token for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":2.08,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The MIBiG Repository is available at https://mibig.secondarymetabolites.org/.","why":"The data availability statement points to a repository with a URL, which is a public repository link (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"There is no access restriction for academic or commercial use of the repository and its data.","why":"The text explicitly states 'no access restriction', which is a synonym for open access, so an access-level label is present. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The source code components, JSON-formatted data standard, and SQL schema for the MIBiG Repository are available on GitHub","why":"A JSON schema and SQL schema are named as documentation objects that travel with the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human-subject data and no gatekeeper is named in the text.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for an external resource (e.g., database accession, RRID) is given in the text. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not mention any retention period, persistence commitment, or availability timing for the data.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:49:04.060563Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}