Data citation question
Yamada, Hiroshi (HSC)
Dear cBioportal officer,
We have a question about how we can refer to the use of cbioportal datasets in a paper and properly cite your datasets.
We downloaded colon cancer datasets for our omics analysis and submitted the results for publication. In the manuscript, we referenced the data as follows:
“Availability of Data and Materials
We obtained original tumor data from the cBioportal (https://www.cbioportal.org/study/summary?id=coadread_tcga_pan_can_atlas_2018) [27,28], which is a publicly available database. Main data generated or analyzed during this study are included in this published article and its supplementary information files. All the datasets used and/or analyzed during the current study will be available from the corresponding author on reasonable request.”
The editorial office was not satisfied, and pasted this guidance:
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As your data falls under the list of data types which must be deposited (listed below), we ask that you please provide the relevant accession numbers and the name of the database in which your
data is stored. If the data has not yet been deposited, please do so and provide the relevant information needed to access it in the “Availability of data and materials” section in your manuscript.
Please ensure all data is already released and that any accession numbers/web links are in the “Availability of Data and Materials” in their final form, and that all web links and accessions
allow access to public data. Please see here for a list of recommended repositories for each data type:
http://www.springernature.com/gp/group/data-policy/repositories
Please note that SciRep mandates data deposition for the following:
• Proteomics data and Protein sequences – can be deposited in Uniprot or PRIDE
• DNA and RNA sequences – can be deposited in any INSDC member repository
• Genetic polymorphisms – can be deposited in dbSNP, dbVar, clinVAR or European Variation Archive (EVA)
• Linked genotype and phenotype data – can be deposited in dbGAP or The European Genome-phenome Archive (EGA)
• Macromolecular structure – can be deposited in the Worldwide Protein Data Bank (wwPDB), the Biological Magnetic Resonance Data Bank (BMRB) or Electron Microscopy Data Bank (EMDB)
• Gene expression data - can be deposited in Gene Expression Omnibus (GEO) or ArrayExpress
• Crystallographic data for small molecules – can be deposited in Crystallography Open Database (COD)
Your availability of data and materials statement can take the following form: “The datasets generated and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK OR ACCESSION NUMBER TO DATASETS]”.
For the omics analysis, we did not generate original sequencing data. Could you advise how to properly cite the cbioportal data and how we can address the referencing format to the editors at springer-nature publisher? As we recall, we did not receive any reference number to cite for the downloaded datasets.
I appreciate your advice and guidance in advance.
Regards,
Hiroshi
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Hiroshi Y. Yamada, Ph.D.
Assistant Professor, Department of Medicine, Hematology-Oncology Section
Associate Member, Center for Cancer Prevention and Drug Development (CCPDD), Stephenson Cancer Center [State’s only NCI designation]
University of Oklahoma Health Sciences Center (OUHSC), P.O. Box 26901
975 NE 10th Street, BRC 1207
Oklahoma City, OK 73104
Fax: (405) 271-3225
Email: hiroshi...@ouhsc.edu
NCBI publication link https://www.ncbi.nlm.nih.gov/myncbi/1-W2e40H80nQg/bibliography/public/
ORCID: https://orcid.org/0000-0002-0536-5581
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