Smoking habit and long-term colorectal cancer incidence by exome-wide mutational and neoantigen loads: evidence based on the prospective cohort incident-tumour biobank method

“Data are available on reasonable request.”

The statement exists and points to a person (Colavizza category 1), which is class 2 (partial). [majority verdict 'partial' (3/5 passes agreed)]

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

“"During 3 473 441 person-years follow-up of 131 140 participants, we documented 3053 colorectal cancer cases including 752 cases with available WES data, which yielded e-TMB (non-synonymous mutation count per megabase; median, 1.6; IQR, 1.0–3.5 and total range, 0–152.0) and neoantigen loads (median, 202; IQR, 137–326 and total range, 0–11,110)."”— not found in the paper; verdict downgraded

The dataset's content is described in running prose, not in an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper]

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'

“"With input from and approval of the External Advisory Committees for the two cohorts (the Nurses’ Health Study (NHS) and the Health Professionals Follow-up Study (HPFS)), we have adopted a data enclave approach to data sharing. Along with a general description of the NHS and HPFS cohorts as well as all questionnaires that have been used since 1976 in the NHS and since 1986 in the HPFS, for both the blood repository and the questionnaire data, guidelines are available on our website for outside users to access the resources of our study ( http://www.nurseshealthstudy.org/ , http://www.hsph.harvard.edu/hpfs/ ). Typically, an outside user prepares a brief proposal that is reviewed by the NHS and HPFS investigator groups to identify a local investigator to assist the outside investigator."”— not found in the paper; verdict downgraded

The text describes an access action (proposal review) but does not label the access level with a standard term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]

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

“"Typically, an outside user prepares a brief proposal that is reviewed by the NHS and HPFS investigator groups to identify a local investigator to assist the outside investigator."”— not found in the paper; verdict downgraded

An institutional gatekeeper (investigator groups and committees) is named for accessing human-subject data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]

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

Neither a persistence commitment nor an availability timing statement is given for the data.

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'

No data or metadata community standard (e.g., MIAME, BIDS, an ontology) is named; only molecular pathology markers are used.

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'

No identifier (accession, DOI, RRID, build ID) for an external resource is provided in the text.

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'

“To further filter out spurious single-nucleotide variant calls, we used BWA (Burrows-Wheeler Aligner)-MEM ( http://bio-bwa.sourceforge.net/ ) to realign sequenced reads associated with the mutations to a set of sequences derived from the human reference assembly.”

The text names specific software (BWA-MEM) and also mentions NetMHCpan V.4.1, qualifying as class 1 (proper nouns). [majority verdict 'yes' (3/5 passes agreed)]

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

No documentation object (README, codebook) is said to accompany the data, and no variable-definition table exists inside the article.

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