PanCNV-Explorer: Deciphering copy number alterations across human cancers

“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.”— not found in the paper; verdict downgraded

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]

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

“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.”

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)]

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'

“A public instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/.”— not found in the paper; verdict downgraded

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)]

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

The data are aggregated from public sources and are not sensitive human-subject data; no gatekeeper is named.

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

The paper does not mention any retention period or availability timing beyond the present availability.

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'

“we converted all CNV files into the standard Variant Call Format (VCF) [35] terminology for copy number events”

VCF is a community-standard data format, and the paper states it was used. [majority verdict 'yes' (3/5 passes agreed)]

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'

“All downloaded databases were stored in the genome assembly GRCh38.”

The paper references the GRCh38 genome assembly and GENCODE version, which are identifiers for external resources. [majority verdict 'yes' (4/5 passes agreed)]

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 retrieve cancer-specific CNAs, we downloaded copy number segmentation files from The Cancer Genome Atlas (TCGA) from 33 cancer types using the TCGAbiolinks package”— not found in the paper; verdict downgraded

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)]

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, or schema) is named as accompanying the data, and no variable-definition table is 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