{"doi":"10.1093/gigascience/giaf093","title":"The Open Pediatric Cancer Project","abstract":"BACKGROUND: In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present an extension of the OpenPBTA called the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multiomic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA sequencing (RNA-seq) from the Genotype-Tissue Expression and The Cancer Genome Atlas projects, OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). FINDINGS: We utilized Gabriella Miller Kids First workflows to harmonize whole-genome sequencing (WGS), whole exome sequencing (WXS), RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, indels, copy number variants, structural variants, RNA expression, fusions, and splice variants. We integrated summarized Clinical Proteomic Tumor Analysis Consortium whole-cell proteomics and phospho-proteomics data and miRNA sequencing data, as well as developed a methylation array harmonization workflow to include m-values, beta-values, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules, which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub) and queryable through PedcBioPortal and the National Cancer Institute's pediatric Molecular Targets Platform. Notably, we have expanded Pediatric Brain Tumor Atlas molecular subtyping to include methylation information to align with the World Health Organization 2021 Central Nervous System Tumor classifications, allowing us to create research-grade integrated diagnoses for these tumors. CONCLUSIONS: OpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.","journal":"GigaScience","year":2025,"id":515213,"datarank":0.3017061074162296,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.009819585057932557,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.009819585057932557,"corpus_percentile":45.17676181635337,"corpus_rank":7088,"citation_count":6,"citer_count":3,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9498,"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":45.8333,"fair_percentile":59.49250993579945,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":32694,"name":"Eric Wafula","orcid":"0000-0001-8073-3797","position":1,"is_corresponding":false},{"id":35783,"name":"Ryan J. Corbett","orcid":"0000-0002-3478-0784","position":2,"is_corresponding":false},{"id":811036,"name":"Yuanchao Zhang","orcid":"0000-0001-8191-4899","position":3,"is_corresponding":false},{"id":32645,"name":"Run Jin","orcid":"0000-0002-8958-9266","position":4,"is_corresponding":false},{"id":29515,"name":"Krutika S. Gaonkar","orcid":"0000-0003-0838-2405","position":5,"is_corresponding":false},{"id":1326865,"name":"Sangeeta Shukla","orcid":"0000-0002-3727-9602","position":6,"is_corresponding":false},{"id":29516,"name":"Komal S. Rathi","orcid":"0000-0001-5534-6904","position":7,"is_corresponding":false},{"id":1326866,"name":"Dave Hill","orcid":"0000-0002-1337-1789","position":8,"is_corresponding":false},{"id":1325853,"name":"Aditya Lahiri","orcid":"0000-0001-9352-1312","position":9,"is_corresponding":false},{"id":32649,"name":"Daniel P. Miller","orcid":"0000-0002-2032-4358","position":10,"is_corresponding":false},{"id":1326867,"name":"Alex Sickler","orcid":"0000-0001-7830-7537","position":11,"is_corresponding":false},{"id":575967,"name":"Kelsey Keith","orcid":"0000-0002-7451-5117","position":12,"is_corresponding":false},{"id":32688,"name":"Christopher Blackden","orcid":"0000-0002-4928-090X","position":13,"is_corresponding":false},{"id":377102,"name":"Antonia Chroni","orcid":"0000-0003-3655-8252","position":14,"is_corresponding":false},{"id":32695,"name":"Miguel A. Brown","orcid":"0000-0001-6782-1442","position":15,"is_corresponding":false},{"id":32666,"name":"Adam A. Kraya","orcid":"0000-0002-8526-5694","position":16,"is_corresponding":false},{"id":1112805,"name":"Kaylyn Clark","orcid":"0000-0002-7207-6608","position":17,"is_corresponding":false},{"id":32663,"name":"Brian R. Rood","orcid":null,"position":18,"is_corresponding":false},{"id":32696,"name":"Adam C. Resnick","orcid":"0000-0003-0436-4189","position":19,"is_corresponding":false},{"id":32684,"name":"Nicholas Van Kuren","orcid":"0000-0002-7414-9516","position":20,"is_corresponding":false},{"id":240511,"name":"John M. Maris","orcid":"0000-0002-8088-7929","position":21,"is_corresponding":false},{"id":289102,"name":"Alvin Farrel","orcid":"0000-0003-1087-9840","position":22,"is_corresponding":false},{"id":32652,"name":"Mateusz P. Koptyra","orcid":"0000-0002-3857-6633","position":23,"is_corresponding":false},{"id":1327326,"name":"Gerri Trooskin","orcid":null,"position":24,"is_corresponding":false},{"id":32687,"name":"Noel Coleman","orcid":"0000-0001-6454-1285","position":25,"is_corresponding":false},{"id":32646,"name":"Yuankun Zhu","orcid":"0000-0002-2455-9525","position":26,"is_corresponding":false},{"id":1327327,"name":"Stephanie Stefankiewicz","orcid":null,"position":27,"is_corresponding":false},{"id":240507,"name":"Zied Abdullaev","orcid":"0000-0001-6345-2088","position":28,"is_corresponding":false},{"id":797246,"name":"Asif Chinwalla","orcid":"0000-0001-7831-3996","position":29,"is_corresponding":false},{"id":32654,"name":"Mariarita Santi","orcid":"0000-0002-6728-3450","position":30,"is_corresponding":false},{"id":381297,"name":"Ammar S. Naqvi","orcid":"0000-0002-0625-666X","position":31,"is_corresponding":false},{"id":32690,"name":"Jennifer L. Mason","orcid":"0000-0001-5884-2815","position":32,"is_corresponding":false},{"id":32692,"name":"Carl J. Koschmann","orcid":"0000-0002-0825-7615","position":33,"is_corresponding":false},{"id":32671,"name":"Xiaoyan Huang","orcid":"0000-0001-7267-4512","position":34,"is_corresponding":false},{"id":32676,"name":"Sharon J. Diskin","orcid":"0000-0002-7200-8939","position":35,"is_corresponding":false},{"id":13200,"name":"Kenneth Aldape","orcid":"0000-0001-5119-7550","position":36,"is_corresponding":false},{"id":32648,"name":"Bailey K. Farrow","orcid":"0000-0001-6727-6333","position":37,"is_corresponding":false},{"id":108218,"name":"Weiping Ma","orcid":"0000-0003-3786-7460","position":38,"is_corresponding":false},{"id":32672,"name":"Bo Zhang","orcid":"0000-0002-0743-5379","position":39,"is_corresponding":false},{"id":32674,"name":"Brian M. Ennis","orcid":"0000-0002-2653-5009","position":40,"is_corresponding":false},{"id":273631,"name":"Sarah K. Tasian","orcid":"0000-0003-1327-1662","position":41,"is_corresponding":false},{"id":944327,"name":"Saksham Phul","orcid":"0000-0002-2771-2572","position":42,"is_corresponding":false},{"id":904781,"name":"Matthew R. Lueder","orcid":"0009-0002-7370-102X","position":43,"is_corresponding":false},{"id":1166380,"name":"Chuwei Zhong","orcid":"0000-0003-2406-2735","position":44,"is_corresponding":false},{"id":282949,"name":"Joseph M. Dybas","orcid":"0000-0001-6700-3378","position":45,"is_corresponding":false},{"id":1379443,"name":"Pei Wang","orcid":"0000-0002-8149-756X","position":46,"is_corresponding":false},{"id":44534,"name":"Deanne Taylor","orcid":"0000-0002-3302-4610","position":47,"is_corresponding":false},{"id":29525,"name":"Hakon Hakonarson","orcid":"0000-0003-2171-3627","position":48,"is_corresponding":false},{"id":814508,"name":"Zhuangzhuang Geng","orcid":"0009-0007-6883-0691","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-19T02:48:39.436300Z","pmid":"40891528","pmcid":"PMC12402770","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":27.7778,"fair_a":12.5,"fair_i":100.0,"fair_r":83.3333,"fair_zscore":0.4506,"fair_rationale":{"fair_score":45.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":27.78,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Merged summary files for the latest release of OpenPedCan are openly accessible in CAVATICA [37] or via download-data.sh script in the OpenPedCan-analysis repository [77].","grounded":false,"rationale":"The paper gives a URL (CAVATICA link) as the location of the data, not a persistent identifier scheme. 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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":"OpenPedCan contains multiomic data from 7 cohorts of pediatric tumors (A, B) with counts by tumor event, RNA-seq from adult tumors from The Cancer Genome Atlas (TCGA) Program (C, D), and RNA-seq from normal adult tissues from the Genotype-Tissue Expression (GTeX) project (E) with counts by specimen.","why":"The dataset content is described in running prose, not in an itemised inventory such as a table or section with file listings. [majority verdict 'partial' (3/5 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":"Merged summary files for the latest release of OpenPedCan are openly accessible in CAVATICA [37] or via download-data.sh script in the OpenPedCan-analysis repository [77].","why":"The paper applies the natural-language label 'openly accessible' to the data, which is equivalent to 'open access'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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":"Biospecimen-level metadata and clinical data are contained in Supplementary Table S1.","why":"Variable definitions are provided in a supplementary table within the article, not in a separate documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper]","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 paper integrates only summary-level outputs and does not require any gatekeeper. [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 state any temporal commitment about how long the data will be available.","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.","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.","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.","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.","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."],"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":"2026-07-20T12:49:20.180916Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}