{"doi":"10.1093/nar/gkaf952","title":"OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis","abstract":"OncoDB was initially developed to advance cancer research by integrating RNA expression profiles, DNA methylation patterns, clinical annotations, and oncoviral signatures derived from the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression datasets. We now present OncoDB 2.0, an extensively expanded platform that offers a more comprehensive and integrated view of cancer omics. The updated version includes an atlas of somatic mutations discovered from combined DNA and RNA sequencing, enabling in-depth investigation of mutation patterns across tumor types and their association with clinical features. Furthermore, we have integrated proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and chromatin accessibility data from TCGA, offering new dimensions for oncogene regulation studies. OncoDB 2.0 also introduces advanced multi-omics analysis modules that facilitate the combined exploration of RNA expression, DNA methylation, and somatic mutations, allowing researchers to examine complex cross-omic relationships with greater depth and flexibility. Together, these enhancements make OncoDB 2.0 a robust and invaluable tool for the cancer research community. OncoDB 2.0 is freely available at https://oncodb.org.","journal":"Nucleic Acids Research","year":2025,"id":522116,"datarank":0.3242217580000735,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.05545783761586524,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.05545783761586524,"corpus_percentile":47.34277094453469,"corpus_rank":6808,"citation_count":5,"citer_count":5,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9357,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":335042,"name":"Gongyu Tang","orcid":"0000-0002-9827-5170","position":1,"is_corresponding":false},{"id":1393525,"name":"Charles S Rogers","orcid":null,"position":2,"is_corresponding":false},{"id":1393526,"name":"Makayla Dove","orcid":null,"position":3,"is_corresponding":false},{"id":872484,"name":"Xinyi Liu","orcid":"0000-0003-0241-5499","position":4,"is_corresponding":false},{"id":1393019,"name":"Yuanxiang Li","orcid":"0000-0001-8917-9294","position":5,"is_corresponding":false},{"id":291574,"name":"Xiaowei Wang","orcid":"0000-0001-9447-4685","position":6,"is_corresponding":false},{"id":618508,"name":"Minsu Cho","orcid":"0000-0003-2498-1109","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":null,"created_at":"2026-07-19T02:49:49.198144Z","pmid":"40995640","pmcid":"PMC12808538","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":75.0,"fair_i":0.0,"fair_r":25.0,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"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":"OncoDB 2.0 is freely available at https://oncodb.org","grounded":true,"rationale":"The identifier given is a web URL (https://oncodb.org), not a persistent identifier scheme like 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":"OncoDB 2.0 is freely available at https://oncodb.org","grounded":true,"rationale":"The named holder is the platform OncoDB 2.0, which is a website, not a repository listed in re3data/FAIRsharing.","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":"Data availability All data in OncoDB are freely accessible at https://oncodb.org","grounded":true,"rationale":"The statement points to a URL (the platform homepage) rather than a repository record with an accession, so it is a link but not a repository record.","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":"OncoDB 2.0 now jointly integrates both DNA- and RNA-derived somatic mutation data, empowering users to examine gene-specific mutation profiles, identify significantly mutated genes, and assess their clinical and prognostic significance across diverse cancer types.","grounded":true,"rationale":"The paper describes the dataset's content in running prose rather than an itemised inventory (table, section, list). 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[majority verdict 'no' (3/5 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; the CC BY-NC license applies to the article only.","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":"RNA-seq reads were aligned to GRCh38.d1 using STAR","grounded":true,"rationale":"The paper names specific software tools (STAR, GATK, BWA-MEM, etc.) used to produce the data. 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'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; the CC BY-NC license applies to the article only.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"OncoDB 2.0 is freely available at https://oncodb.org","why":"The identifier given is a web URL (https://oncodb.org), not a persistent identifier scheme like 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. 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Prefer open proteomics formats such as mzML or mzIdentML.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format token for the released data is named in the text.","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. 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Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"OncoDB 2.0 is freely available at https://oncodb.org","why":"The dataset identifier (URL) appears only in body text, not in the reference list.","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 for the data snapshot is provided; 'OncoDB 2.0' refers to the platform version. [majority verdict 'no' (2/5 passes agreed)]","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":"partial","current":0.5,"evidence":"Data availability All data in OncoDB are freely accessible at https://oncodb.org","why":"The statement points to a URL (the platform homepage) rather than a repository record with an accession, so it is a link but not a repository record.","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. 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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 (accession, DOI, RRID) for a non-own resource (e.g., source dataset, database) is provided in the text. [majority verdict 'no' (3/5 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":"No temporal commitment or retention period is stated for the data. [majority verdict 'no' (3/5 passes agreed)]","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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. 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Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:58:25.488373Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}