{"doi":"10.1093/nar/gkae1085","title":"Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes","abstract":"The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes.","journal":"Nucleic Acids Research","year":2024,"id":421218,"datarank":0.6991424737616678,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.17928208834170872,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.17928208834170872,"corpus_percentile":71.40094376112013,"corpus_rank":3698,"citation_count":31,"citer_count":27,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.947,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":70.8333,"fair_percentile":91.99021705900336,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1214055,"name":"Susie Huget","orcid":null,"position":1,"is_corresponding":false},{"id":1214056,"name":"Juan Jose Medina Reyes","orcid":null,"position":2,"is_corresponding":false},{"id":614236,"name":"Eliot Ragueneau","orcid":"0000-0002-7876-6503","position":3,"is_corresponding":false},{"id":560412,"name":"Kalpana Panneerselvam","orcid":"0000-0003-2534-198X","position":4,"is_corresponding":false},{"id":1214057,"name":"Samantha N Fischer","orcid":null,"position":5,"is_corresponding":false},{"id":1214058,"name":"Erin R Claussen","orcid":null,"position":6,"is_corresponding":false},{"id":1213361,"name":"Savvas Kourtis","orcid":"0000-0002-3800-0853","position":7,"is_corresponding":false},{"id":617740,"name":"Colin Combe","orcid":"0000-0003-2526-2587","position":8,"is_corresponding":false},{"id":95742,"name":"Birgit H M Meldal","orcid":"0000-0003-4062-6158","position":9,"is_corresponding":false},{"id":12455,"name":"Livia Perfetto","orcid":"0000-0003-4392-8725","position":10,"is_corresponding":false},{"id":351338,"name":"Juri Rappsilber","orcid":"0000-0001-5999-1310","position":11,"is_corresponding":false},{"id":1213362,"name":"Georg Kustatscher","orcid":"0000-0001-8955-0866","position":12,"is_corresponding":false},{"id":240126,"name":"Kevin Drew","orcid":"0000-0002-1260-4413","position":13,"is_corresponding":false},{"id":5925,"name":"Sandra Orchard","orcid":"0000-0002-8878-3972","position":14,"is_corresponding":false},{"id":5922,"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","position":15,"is_corresponding":false},{"id":1213360,"name":"Sucharitha Balu","orcid":"0000-0001-7456-0594","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":null,"created_at":"2026-07-19T01:57:36.298171Z","pmid":"39558156","pmcid":"PMC11701666","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":50.0,"fair_a":87.5,"fair_i":20.0,"fair_r":75.0,"fair_zscore":1.4401,"fair_rationale":{"fair_score":70.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data can be accessed either via our ftp site ( ftp.ebi.ac.uk/ pub/ databases/ intact/ complex/ current/) or our REST API ( https://www.ebi.ac.uk/intact/ complex-ws/).","grounded":true,"rationale":"The paper gives a URL (FTP) and a REST API as the data location, not a persistent identifier scheme such as DOI or Handle.","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 Complex Portal ( www.ebi.ac.uk/complexportal ) is a manually curated reference database for molecular complexes.","grounded":false,"rationale":"The paper names the Complex Portal as the database holding the data; it is a recognised data repository. [downgraded to 'partial' — no verifiable quote from the paper]","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":1.0,"verdict":"yes","evidence":"Data can be accessed either via our ftp site ( ftp.ebi.ac.uk/ pub/ databases/ intact/ complex/ current/) or our REST API ( https://www.ebi.ac.uk/intact/ complex-ws/).","grounded":true,"rationale":"The statement points to a public repository (FTP and API) with a link to archived data, matching Colavizza category 3.","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":0.0,"verdict":"no","evidence":"The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0.","grounded":false,"rationale":"The dataset size and content are described in running prose, but there is no itemised inventory like a table or list of files. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":0.5,"verdict":"partial","evidence":"Data can be accessed either via our ftp site ( ftp.ebi.ac.uk/ pub/ databases/ intact/ complex/ current/) or our REST API ( https://www.ebi.ac.uk/intact/ complex-ws/).","grounded":true,"rationale":"The dataset location appears only in the body text (Data availability section), not in the reference list. [majority verdict 'partial' (4/5 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":87.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The Complex Portal is an open source (Apache 2.0), open data (CC0) project","grounded":true,"rationale":"The data are stated to be openly available via FTP and REST API with no precondition.","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":1.0,"verdict":"yes","evidence":"The Complex Portal is an open source (Apache 2.0), open data (CC0) project","grounded":true,"rationale":"The paper explicitly labels the data as 'open data (CC0)', which is an access-level label. [majority verdict 'yes' (4/5 passes agreed)]","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":"The Complex Portal is an open source (Apache 2.0), open data (CC0) project","grounded":true,"rationale":"The data are not sensitive; no gatekeeper is needed, and the text shows open access without any access control.","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":1.0,"verdict":"yes","evidence":"We maintain stable complex and participant identifiers for our curated complexes, and we will extend this practice such that in the event of complexes being deleted from a hu.MAP version, we will continue to maintain them.","grounded":true,"rationale":"The paper commits to persisting identifiers and maintaining data even if external sources delete them, implying indefinite retention.","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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"The FTP site contains files in different formats, grouped by species","grounded":true,"rationale":"No specific format token is named; the paper only mentions 'different formats' without specifying any.","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":0.5,"verdict":"partial","evidence":"Evidence and Conclusion Ontology (ECO) codes (19) are key to describing the weight of evidence","grounded":false,"rationale":"The paper uses the ECO ontology, a community standard registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper]","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":"Developers can contribute to the code at https:// github.com/ Complex- Portal/complex- portal- view (archived at https://doi.org/10.6084/m9.figshare.27284529).","grounded":false,"rationale":"The paper provides a DOI for the code repository, which is a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [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":75.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"open data (CC0)","grounded":true,"rationale":"The paper explicitly states the data are licensed under CC0, an open standard licence. [majority verdict 'yes' (4/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"hu.MAP3.0 (17)","grounded":false,"rationale":"The paper names the specific software pipeline (hu.MAP3.0) used to produce the predicted complexes. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, data dictionary, etc.) is mentioned as accompanying the data. [majority verdict 'no' (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":1.0,"verdict":"yes","evidence":"as of build 247 (20 May 2024)","grounded":true,"rationale":"The paper identifies the dataset snapshot by a build number and a date, which is a version token.","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":1.0,"verdict":"yes","evidence":"Developers can contribute to the code at https:// github.com/ Complex- Portal/complex- portal- view (archived at https://doi.org/10. 6084/m9.figshare.27284529 ).","grounded":true,"rationale":"The paper gives a code repository URL and an archived DOI, both machine-resolvable locators. [majority verdict 'yes' (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":"BBSRC—National Science Foundation / Directorate for Biological Sciences [BB / X002179 / 1, BB / X002683 / 1]","grounded":true,"rationale":"The paper lists specific grant numbers for the funding bodies.","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":"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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data can be accessed either via our ftp site ( ftp.ebi.ac.uk/ pub/ databases/ intact/ complex/ current/) or our REST API ( https://www.ebi.ac.uk/intact/ complex-ws/).","why":"The paper gives a URL (FTP) and a REST API as the data location, not a persistent identifier scheme such as DOI or Handle.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Complex Portal ( www.ebi.ac.uk/complexportal ) is a manually curated reference database for molecular complexes.","why":"The paper names the Complex Portal as the database holding the data; it is a recognised data repository. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","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 genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The FTP site contains files in different formats, grouped by species","why":"No specific format token is named; the paper only mentions 'different formats' without specifying any.","gain":8.33,"priority":"important","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data can be accessed either via our ftp site ( ftp.ebi.ac.uk/ pub/ databases/ intact/ complex/ current/) or our REST API ( https://www.ebi.ac.uk/intact/ complex-ws/).","why":"The dataset location appears only in the body text (Data availability section), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0.","why":"The dataset size and content are described in running prose, but there is no itemised inventory like a table or list of files. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Evidence and Conclusion Ontology (ECO) codes (19) are key to describing the weight of evidence","why":"The paper uses the ECO ontology, a community standard registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"hu.MAP3.0 (17)","why":"The paper names the specific software pipeline (hu.MAP3.0) used to produce the predicted complexes. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"no","current":0.0,"evidence":null,"why":"No documentation object (README, data dictionary, etc.) is mentioned as accompanying the data. [majority verdict 'no' (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. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The Complex Portal is an open source (Apache 2.0), open data (CC0) project","why":"The data are not sensitive; no gatekeeper is needed, and the text shows open access without any access control.","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":"Developers can contribute to the code at https:// github.com/ Complex- Portal/complex- portal- view (archived at https://doi.org/10.6084/m9.figshare.27284529).","why":"The paper provides a DOI for the code repository, which is a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing formats such as FASTQ, BAM or VCF.","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper."],"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":"2026-07-20T11:35:31.292095Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}