{"doi":"10.64898/2026.01.26.701884","title":"PanCNV-Explorer: Deciphering copy number alterations across human cancers","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Copy number variants (CNVs) are major drivers of cancer progression and genetic disorders, yet their interpretation, spanning biological mechanisms, clinical relevance, and therapeutic implications, remains fragmented across disparate resources. To bridge this gap, we present PanCNV-Explorer, a unified database integrating harmonized copy number variation data across 33 cancer types, cancer cell lines, and healthy cohorts. PanCNV-Explorer provides a genome-wide atlas of CNV frequency and functional impact, quantifying tissue-specific amplifications and deletions in both cancer and non-cancer contexts through rigorous cross-dataset normalization. The interactive web interface enables researchers to dynamically query CNVs by genomic coordinates or gene symbol, visualize cancer-type-specific frequencies with real-time comparative analysis, and explore integrated genomic features including transcripts, regulatory elements, and gene expression through a zoomable genome browser. Beyond exploration, the platform offers programmatic APIs for pan-cancer CNV analysis and visualization. A public web instance of PanCNV-Explorer is available at\n                  <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/\">https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/</jats:ext-link>\n                  .\n                </jats:p>","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2026,"id":1852,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9288,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2026-01-27","fair_score":25.0,"fair_percentile":41.022519780888615,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":20785,"name":"Kevin Kornrumpf","orcid":"0009-0007-3229-8592","position":1,"is_corresponding":false},{"id":20786,"name":"Anna-Rosa Krüger","orcid":null,"position":2,"is_corresponding":false},{"id":20787,"name":"Jürgen Dönitz","orcid":"0000-0002-8401-8851","position":3,"is_corresponding":false},{"id":20788,"name":"Nadine Sina Kurz","orcid":null,"position":4,"is_corresponding":false},{"id":20789,"name":"Anna-Rosa Krueger","orcid":null,"position":5,"is_corresponding":false},{"id":20790,"name":"Juergen Doenitz","orcid":null,"position":6,"is_corresponding":false},{"id":20784,"name":"Nadine S. Kurz","orcid":"0000-0001-8857-1534","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"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":11.1111,"fair_a":37.5,"fair_i":100.0,"fair_r":25.0,"fair_zscore":-0.3734,"fair_rationale":{"fair_score":25.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","grounded":false,"rationale":"The paper gives a web address for the data, not a persistent identifier from a PID scheme. [downgraded to 'no' — no verifiable quote from the paper]","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":0.0,"verdict":"no","evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","grounded":false,"rationale":"The data are hosted on an institutional web server, not a named repository from the curated list. [downgraded to 'no' — 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":0.0,"verdict":"no","evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/. The source code of PanCNV-Explorer, including the database generation, the web server, the web front end and the CNA annotation modules, is available at https://gitlab.gwdg.de/MedBioinf/mtb/cnv-database. The annotation modules for CNVs and structural variants were added to the Onkopus framework and are publicly available through APIs at https://mtb.bioinf.med.uni-goettingen.de/onkopus/api. All data sources of the copy number alteration annotation are publicly available.","grounded":false,"rationale":"The data availability statement points to a web instance and code repositories, not to a repository record with an accession, so it is a partial category. [downgraded to 'no' — no verifiable quote from the paper]","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":0.5,"verdict":"partial","evidence":"we created three versions of the database: First, we generated the database according to consensus segments, where we calculated the occurring CNV segments from the existing start and end positions and then applied clustering to reduce the number of CNV segments to 200.000. Second, we computed fixed-sized bins of 10.000 base pairs across the whole genome. And third, we generated gene-level CNV segments, were CNV start and end positions corresponded to the positions of protein-coding genes.","grounded":true,"rationale":"The dataset's content is described in running prose, not in a section, table, or enumerated list, so it is a partial description. [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","grounded":false,"rationale":"The dataset's identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","grounded":false,"rationale":"The data are stated to be publicly available with no stated precondition. [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":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","grounded":false,"rationale":"The paper labels the data as 'public' in the data availability statement, an explicit access-level label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":null,"grounded":false,"rationale":"The data are aggregated from public sources and are not sensitive human-subject data; no gatekeeper is named.","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 or availability timing beyond the present availability.","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":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The completed database is downloadable via the web interface in BED and VCF format.","grounded":true,"rationale":"BED and VCF are open, community-standard file formats.","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":"we converted all CNV files into the standard Variant Call Format (VCF) [35] terminology for copy number events","grounded":true,"rationale":"VCF is a community-standard data format, and the paper states it was used. [majority verdict 'yes' (3/5 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":1.0,"verdict":"yes","evidence":"All downloaded databases were stored in the genome assembly GRCh38.","grounded":true,"rationale":"The paper references the GRCh38 genome assembly and GENCODE version, which are identifiers for external resources. [majority verdict 'yes' (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":25.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license for the data is stated anywhere in the text.","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":"To retrieve cancer-specific CNAs, we downloaded copy number segmentation files from The Cancer Genome Atlas (TCGA) from 33 cancer types using the TCGAbiolinks package","grounded":false,"rationale":"The paper names specific tools and databases (TCGAbiolinks, TCGA, etc.) used to produce the data. [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, codebook, or schema) is named as accompanying the data, and no variable-definition table is inside the article.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given for the dataset itself.","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 of PanCNV-Explorer, including the database generation, the web server, the web front end and the CNA annotation modules, is available at https://gitlab.gwdg.de/MedBioinf/mtb/cnv-database.","grounded":false,"rationale":"The paper provides a GitLab URL for the source code, a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper]","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":"This work was supported by the Gemeinsamer Bundesauschuss (01NVF20006), the Volkswagen Foundation (11-76251-12-1/19), the Deutsche Krebshilfe (70114018), the Deutsche Forschungsgemeinschaft (KFO5002) and the Bundesministerium für Bildung und Forschung (BMBF) (01KD2437, 01KD2401B, 01KD2208A, 01KD2414A).","grounded":true,"rationale":"The paper lists specific award numbers for each funder.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","why":"The paper gives a web address for the data, not a persistent identifier from a PID scheme. [downgraded to 'no' — no verifiable quote from the paper]","gain":16.67,"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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","why":"The data are hosted on an institutional web server, not a named repository from the curated list. [downgraded to 'no' — no verifiable quote from the paper]","gain":16.67,"priority":"essential","scored":true},{"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":"No license for the data is stated anywhere in the text.","gain":16.67,"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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","why":"The data are stated to be publicly available with no stated precondition. [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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","why":"The dataset's identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"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 of PanCNV-Explorer, including the database generation, the web server, the web front end and the CNA annotation modules, is available at https://gitlab.gwdg.de/MedBioinf/mtb/cnv-database.","why":"The paper provides a GitLab URL for the source code, a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper]","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":"no","current":0.0,"evidence":null,"why":"No version token or date is given for the dataset itself.","gain":4.17,"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":"no","current":0.0,"evidence":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/. The source code of PanCNV-Explorer, including the database generation, the web server, the web front end and the CNA annotation modules, is available at https://gitlab.gwdg.de/MedBioinf/mtb/cnv-database. The annotation modules for CNVs and structural variants were added to the Onkopus framework and are publicly available through APIs at https://mtb.bioinf.med.uni-goettingen.de/onkopus/api. All data sources of the copy number alteration annotation are publicly available.","why":"The data availability statement points to a web instance and code repositories, not to a repository record with an accession, so it is a partial category. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"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":"partial","current":0.5,"evidence":"we created three versions of the database: First, we generated the database according to consensus segments, where we calculated the occurring CNV segments from the existing start and end positions and then applied clustering to reduce the number of CNV segments to 200.000. Second, we computed fixed-sized bins of 10.000 base pairs across the whole genome. And third, we generated gene-level CNV segments, were CNV start and end positions corresponded to the positions of protein-coding genes.","why":"The dataset's content is described in running prose, not in a section, table, or enumerated list, so it is a partial description. [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":"A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.","why":"The paper labels the data as 'public' in the data availability statement, an explicit access-level label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"To retrieve cancer-specific CNAs, we downloaded copy number segmentation files from The Cancer Genome Atlas (TCGA) from 33 cancer types using the TCGAbiolinks package","why":"The paper names specific tools and databases (TCGAbiolinks, TCGA, etc.) used to produce 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":"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, codebook, or schema) is named as accompanying the data, and no variable-definition table is inside the article.","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 clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are aggregated from public sources and are not sensitive human-subject data; no gatekeeper is named.","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 or availability timing beyond the present availability.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) 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":"2026-07-20T13:59:48.628256Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}