Data, knowledge, and tools within the AKC are provided as a public resource. When publishing or presenting AKC content or research findings derived from it, please cite the AKC, the data repository contributing data to the AKC, and the original data generators, as appropriate. These citations help us demonstrate to our funders that these resources are worth funding.
- Please cite the AKC using the URL: https://airr-knowledge.org
- If you draw detailed analysis from specific sources (repertoires or genomic studies), please cite the studies concerned.
- If you are citing the AKC component repositories, list for each below:
AIRR Data Commons: Christley, S., Aguiar, A., Blanck, G., Breden, F., Bukhari, S. A. C., Busse, C. E., Jaglale, J., Harikrishnan, S. L., Laserson, U., Peters, B., Rocha, A., Schramm, C. A., Taylor, S., Vander Heiden, J. A., Zimonja, B., Watson, C. T., Corrie, B., & Cowell, L. G. (2020). The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Frontiers in Big Data, 3. doi.org/10.3389/fdata.2020.00022. PMID: 33693395; PMCID: PMC7931935.
VDJServer: Christley, S., Scarborough, W., Salinas, E., Rounds, W. H., Toby, I. T., Fonner, J. M., Levin, M. K., Kim, M., Mock, S. A., Jordan, C., Ostmeyer, J., Buntzman, A., Rubelt, F., Davila, M. L., Monson, N. L., Scheuermann, R. H., & Cowell, L. G. (2018). VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Frontiers in Immunology, 9. doi.org//10.3389/fimmu.2018.00976. PMID: 29867956; PMCID: PMC5953328.
iReceptor: Corrie, B. D., Marthandan, N., Zimonja, B., Jaglale, J., Zhou, Y., Barr, E., Knoetze, N., Breden, F. M. W., Christley, S., Scott, J. K., Cowell, L. G., & Breden, F. (2018). iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. Immunological Reviews, 284(1), 24–41. doi.org/10.1111/imr.12666. PMID:29944754.
OGRDB: Lees, W., Busse, C. E., Corcoran, M., Ohlin, M., Scheepers, C., Matsen, F. A., IV, Yaari, G., Watson, C. T., The AIRR Community, Collins, A., & Shepherd, A. J. (2020). OGRDB: A reference database of inferred immune receptor genes. Nucleic Acids Research, 48(D1), D964–D9700, doi.org/10.1093/nar/gkz822
- If you use a germline set in your work, please cite as “Germline set xyz version n downloaded from OGRDB” along with the DOI.
VDJbase: Omer, A., Shemesh, O., Peres, A., Polak, P., Shepherd, A. J., Watson, C. T., Boyd, S. D., Collins, A. M., Lees, W., & Yaari, G. (2020). VDJbase: An adaptive immune receptor genotype and haplotype database. Nucleic Acids Research, 48(D1), D1051–D1056. doi.org/10.1093/nar/gkz872
IEDB: Vita, R., Blazeska, N., Marrama, D., Duesing, S., Bennett, J., Greenbaum, J., De Almeida Mendes, M., Mahita, J., Wheeler, D. K., Cantrell, J. R., Overton, J. A., Natale, D. A., Sette, A., & Peters, B. (2024). The Immune Epitope Database (IEDB): 2024 update. Nucleic Acids Research, 53(D1), D436–D443. doi.org/10.1093/nar/gkae1092