The AD Knowledge Portal: A Repository for Multi‐Omic Data on Alzheimer's Disease and Aging
Open accessAbstract
The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD). In this article, we highlight how to use the Portal to discover and download genomic variant and transcriptomic data from the same individuals. First, we show how to use the web interface to browse and search for data of interest using relevant file annotations. We demonstrate how to learn more about the context surrounding the data, including diagnostic criteria and methodological details about sample preparation and data analysis. We present two primary ways to download data—using a web interface, and using a programmatic method that provides access using the command line. Finally, we show how to merge separate sources of metadata into a comprehensive file that contains factors and covariates necessary in downstream analyses. © 2020 The Authors. Basic Protocol 1: Find and download files associated with a selected study Basic Protocol 2: Download files in bulk using the command line client Basic Protocol 3: Working with file annotations and metadata
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MR1 gene expression is elevated in brain tissue of AD patients, specifically in the temporal cortex, parahippocampal gyrus, and superior temporal gyrus, normalized to age of death.
“Having found that MR1 gene expression is elevated in the brain tissue of AD patients by mining the Agora database”
From Control of the temporal development of Alzheimer’s disease pathology by the MR1/MAIT cell axis (2023) · cites this paper as [23]
The Introduction describes the AD Knowledge Portal as a repository containing transcriptomic data from human brain samples, but it reports no MR1 expression result. Searches of our copy for MR1, Agora, the named brain regions, and age-of-death normalization found no passage addressing the claimed elevation. (LLM, conf=0.75)
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Cites
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., et al. (2019) · Journal of Open Source Software · doi:10.21105/joss.01686 · Cited by 22,138 · see citing works
Self-citationThe FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423 · see citing works
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Research works printed but not linked: 2
- Friend, S., & Norman, T. (2013). Metcalfe's law and the biology information commons. Nature Biotechnology, 31, 297– 303. doi: 10.1038/nbt.2555. 23563423 · DOI
- Hodes, R. J., & Buckholtz, N. (2016). Accelerating medicines partnership: Alzheimer's disease (AMP‐AD) knowledge portal aids Alzheimer's drug discovery through open data sharing, Expert Opinion on Therapeutic Targets, 20, 389– 391. doi: 10.1517/14728222.2016.1135132. 26853544 · DOI
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Iturria-Medina, Y., Adewale, Q., Khan, A. F., Ducharme, S., Rosa-Neto, P., O’Donnell, K., Petyuk, V. A., Gauthier, S., De Jager, P. L., Breitner, J., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo6764 · Cited by 100 · see citing works
Artificial intelligence for drug discovery and development in Alzheimer's disease
Qiu, Y., & Cheng, F. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102776 · Cited by 83 · see citing works
Cheng, F., Wang, F., Tang, J., Zhou, Y., Fu, Z., Zhang, P., Haines, J. L., Leverenz, J. B., Gan, L., Hu, J., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101379 · Cited by 63 · see citing works
Tripathy, R. K., Frohock, Z., Wang, H., Cary, G. A., Keegan, S., Carter, G. W., & Li, Y. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00519-9 · Cited by 36 · see citing works
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Self-citationOblak, A. L., Kotredes, K. P., Pandey, R. S., Reagan, A. M., Ingraham, C., Perkins, B., Lloyd, C., Baker, D., Lin, P. B., Soni, D. M., et al. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.886575 · Cited by 23 · see citing works
“More details on strain creation are provided on the AD Knowledge Portal.”
MethodInfluentialControl of the temporal development of Alzheimer’s disease pathology by the MR1/MAIT cell axis
Wyatt-Johnson, S. K., Kersey, H. N., Codocedo, J. F., Newell, K. L., Landreth, G. E., Lamb, B. T., Oblak, A. L., & Brutkiewicz, R. R. (2023) · Journal of Neuroinflammation · doi:10.1186/s12974-023-02761-6 · Cited by 22 · see citing works
“Interestingly, in accessing the Agora AD database which was generated from over 1100 individuals [22, 23], we found that MR1 gene expression is increased in the temporal cortex, parahippocampal gyrus, and superior temporal gyrus in AD patients normalized to the age of death (Fig.”
MethodTowards an AI biomedical scientist: Accelerating discoveries in neurodegenerative disease
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- Authors
- Greenwood, A. K., Montgomery, K. S., Kauer, N., Woo, K. H., Leanza, Z. J., Poehlman, W. L., Gockley, J., Sieberts, S. K., Bradic, L., Logsdon, B. A., Peters, M. A., Omberg, L., & Mangravite, L. M.
- Affiliations
- Sage Bionetworks (US)
- Sage Bionetworks Seattle Washington
- Corresponding author
- Mangravite, Lara M.
- ORCID
- Venue
- Current Protocols in Human Genetics
- Publisher
- Wiley
- Published
- 2020-10-21
- Volume
- 108
- Issue
- 1
- Pages
- e105-e105
- ISSN
- 1934-8258 (ISSN-L)
- 1934-8266
- PMC
- PMC7587039
- OpenAlex
- W3093800747
- Cited by
- 102
- References
- 2
- Citations by year
- 2026: 15 · 2025: 24 · 2024: 23 · 2023: 24 · 2022: 12 · 2021: 4
- FWCI
- 6.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Current Protocols in Human Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- National Institute on Aging (U24AG061340, U01AG046139, U01AG046152, U01AG046161, U01AG046170, R01AG046171, R01AG046174, RF1AG051556, RF1AG051633, RF1AG051504, RF1AG051550, R01NS096730, P50AG016574, R37AG027924)
- Cure Alzheimer's Fund
- Mayo Foundation for Medical Education and Research
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- Alzheimer's disease, aging, dementia, genomic variant data, transcriptomic data, data download, web interface
- MeSH terms
- Aging, Alzheimer Disease, Humans, Software, Information Storage and Retrieval, Internet, Genomics, Databases, Genetic
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