Appendix A — Data Acquisition References

Published

Jun 2026

This guide draws upon public repository documentation, metadata standards, reproducibility frameworks, and data-sharing initiatives that support modern omics data acquisition workflows.

The references cited throughout this guide are maintained in the bibliography database (library/references.bib) and are included automatically during book generation.

Suggested Citation Keys

The following citation keys are commonly used throughout the CDI Data Acquisition System:

Major Public Data Resources

NCBI: https://www.ncbi.nlm.nih.gov (National Center for Biotechnology Information 2026d)
Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra (National Center for Biotechnology Information 2026e)
BioProject: https://www.ncbi.nlm.nih.gov/bioproject (National Center for Biotechnology Information 2026a)
BioSample: https://www.ncbi.nlm.nih.gov/biosample (National Center for Biotechnology Information 2026b)
Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo (National Center for Biotechnology Information 2026c)
European Nucleotide Archive (ENA): https://www.ebi.ac.uk/ena (European Nucleotide Archive 2026)
MGnify: https://www.ebi.ac.uk/metagenomics (European Bioinformatics Institute 2026b)
GWAS Catalog: https://www.ebi.ac.uk/gwas (European Bioinformatics Institute 2026a)
DNA Data Bank of Japan (DDBJ): https://www.ddbj.nig.ac.jp (DNA Data Bank of Japan 2026)

Arita, M., I. Karsch-Mizrachi, and G. Cochrane. 2021. “The International Nucleotide Sequence Database Collaboration.” Nucleic Acids Research 49 (D1): D121–24.

Barrett, T., S. E. Wilhite, P. Ledoux, et al. 2013. “NCBI GEO: Archive for Functional Genomics Data Sets—Update.” Nucleic Acids Research 41 (Database issue): D991–95.

Brazma, A., P. Hingamp, J. Quackenbush, et al. 2001. “Minimum Information about a Microarray Experiment (MIAME)—Toward Standards for Microarray Data.” Nature Genetics 29 (4): 365–71.

DNA Data Bank of Japan. 2026. “DDBJ.” https://www.ddbj.nig.ac.jp.

European Bioinformatics Institute. 2026a. “GWAS Catalog.” https://www.ebi.ac.uk/gwas.

———. 2026b. “MGnify.” https://www.ebi.ac.uk/metagenomics.

European Nucleotide Archive. 2026. “European Nucleotide Archive (ENA).” https://www.ebi.ac.uk/ena.

Knight, R., A. Vrbanac, B. C. Taylor, et al. 2018. “Best Practices for Analysing Microbiomes.” Nature Reviews Microbiology 16 (7): 410–22.

Kodama, Y., M. Shumway, and R. Leinonen. 2012. “The Sequence Read Archive: Explosive Growth of Sequencing Data.” Nucleic Acids Research 40 (Database issue): D54–56.

Leinonen, R., H. Sugawara, and M. Shumway. 2011. “The Sequence Read Archive.” Nucleic Acids Research 39 (Database issue): D19–21.

Mitchell, A. L., A. Almeida, M. Beracochea, et al. 2020. “MGnify: The Microbiome Analysis Resource in 2020.” Nucleic Acids Research 48 (D1): D570–78.

National Center for Biotechnology Information. 2026a. “BioProject.” https://www.ncbi.nlm.nih.gov/bioproject.

———. 2026b. “BioSample.” https://www.ncbi.nlm.nih.gov/biosample.

———. 2026c. “Gene Expression Omnibus (GEO).” https://www.ncbi.nlm.nih.gov/geo.

———. 2026d. “NCBI.” https://www.ncbi.nlm.nih.gov.

———. 2026e. “Sequence Read Archive (SRA).” https://www.ncbi.nlm.nih.gov/sra.

Sandve, G. K., A. Nekrutenko, J. Taylor, and E. Hovig. 2013. “Ten Simple Rules for Reproducible Computational Research.” PLoS Computational Biology 9 (10): e1003285.

Wilkinson, M. D., M. Dumontier, I. J. Aalbersberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3: 160018.

Yilmaz, P., R. Kottmann, D. Field, et al. 2011. “Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any Sequence (MIxS) Specifications.” Nature Biotechnology 29 (5): 415–20.