Barriers to accessing public cancer genomic data
Open accessAbstract
Although increasingly recognized as critical to genomic research, genomic data sharing is hindered by an absence of standards regarding timing, patient privacy, use agreement standards, and data characterization and quality. Only after months of identifying, permissioning for use, committing to terms restricting use and sharing, downloading, and assessing quality, is it possible to know whether or not a dataset can be used. In this paper, we evaluate the barriers to data sharing based on the Treehouse experience and offer recommendations for use agreement standards, data characterization and metadata standardization to enhance data sharing and outcomes for all pediatric cancer patients.
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Assembling genomic databases and chemical compound or protein structure databases for drug discovery is extremely challenging and could be error ridden because many genomic and protein databases lack necessary annotations, are inconsistent in formats, and may be poor in data quality.
“For example, assembling genomic databases and chemical compound or protein structure databases for drug discovery is extremely challenging and could be error ridden because many genomic and protein databases lack necessary annotations, are inconsistent in formats, and may be poor in data quality [64].”
From Generative AI in medical practice: in-depth exploration of privacy and security challenges (2024) · cites this paper as [64]
Step 4 (Characterizing the data) describes incomplete or erroneous metadata, and Step 5 (Data quality) describes poorly formatted or low-quality cancer genomic data that can prevent analysis. The paper does not establish the same problems for chemical-compound or protein-structure databases, or address assembling those databases for drug discovery. No page numbers are available in our copy. (LLM, conf=0.88)
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Generative AI in medical practice: in-depth exploration of privacy and security challenges
Chen, Y., & Esmaeilzadeh, P. (2024) · Journal of Medical Internet Research · doi:10.2196/53008 · Cited by 353 · see citing works
“…example, assembling genomic databases and chemical compound or protein structure databases for drug discovery is extremely challenging and could be error ridden because many genomic and protein databases lack necessary annotations, are inconsistent in formats, and may be poor in data quality [64].”
- Authors
- Learned, K., Durbin, A., Currie, R., Kephart, E. T., Beale, H. C., Sanders, L. M., Pfeil, J., Goldstein, T. C., Salama, S. R., Haussler, D., Vaske, O. M., & Bjork, I. M.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Learned, Katrina
- Bjork, Isabel M.
- ORCID
- Venue
- Scientific Data
- Published
- 2019-06-20
- Volume
- 6
- Issue
- 1
- Pages
- 98-98
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC6586850
- OpenAlex
- W2951725468
- Cited by
- 34
- References
- 3
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 2 · 2023: 3 · 2022: 4 · 2021: 10 · 2020: 6 · 2019: 1
- Type
- data paper
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Data (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute (427053)
- St. Baldrick's Foundation (427053)
- Topics
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Ethics in Clinical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- data sharing, data access barriers, patient privacy, metadata standardization, data quality, childhood cancer, treehouses, data characterization
- MeSH terms
- Humans, Neoplasms, Genomics, Information Dissemination, Datasets as Topic
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