Amazon Biobank: a Blockchain-based Genomic Database for Bioeconomy
Resumo
The bioeconomy, an industrial production model based on biological resources and sustainable development, can be considered an emerging opportunity for biodiversity-abundant regions, such as the Amazon rainforest. However, existing genomic repositories lack data traceability and economic benefit-sharing mechanisms, resulting in limited motivation for data providers to contribute. To address this challenge, we present Amazon Biobank, a community-driven genetic database. By leveraging blockchain and peer-to-peer (P2P) technologies, we enable distributed and transparent data sharing; meanwhile, by using smart contracts directly registered in the system, we enforce fair benefit-sharing among all system participants. Moreover, Amazon Biobank is designed to be auditable by any user, reducing the need for trusted system managers. To validate our approach, we implemented a prototype using Hyperledger Fabric and BitTorrent and evaluated its performance. Our results show that the prototype can support at least 400 transactions per second in a small network and that it can be further improved by adding new nodes or allocating additional computational resources. We expect that Amazon Biobank will serve as a vital tool for collaborative biotechnology research, fostering sustainable development in high-biodiversity regions.
Palavras-chave:
biodiversity, Benefit-sharing, DNA sequencing, sustainable development, Blockchain, Smart contract, DNA database
Referências
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Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A., Anderson, C. L., Figueiredo, J. P., Jaramillo, C., Riff, D., Negri, F. R., Hooghiemstra, H., Lundberg, J., Stadler, T., Särkinen, T., and Antonelli, A. (2010). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science, 330(6006):927–931.
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Kimura, L. T., Andrade, E. R., Nobre, I., Nobre, C. A., de Medeiros, B. A. S., Riaño-Pachón, D. M., Shiraishi, F. K., Carvalho, T. C. M. B., and Simplicio, M. A. (2023). Amazon biobank: a collaborative genetic database for bioeconomy development. Functional & Integrative Genomics, 23(2):101.
Kulemin, N., Popov, S., and Gorbachev, A. (2017). The zenome project: Whitepaper blockchain-based genomic ecosystem. Zenome. io, page A.
Li, F.-W. (2021). Decolonizing botanical genomics. Nature Plants, 7(12):1542–1543.
Mgbeoji, I. (2007). Global biopiracy: patents, plants, and indigenous knowledge. ubc Press.
Nobre, C. A., Sampaio, G., Borma, L. S., Castilla-Rubio, J. C., Silva, J. S., and Cardoso, M. (2016). Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm. Proc. of the National Academy of Sciences, 113(39):10759–10768.
Nobre, I. and Nobre, C. A. (2019). The Amazonia third way initiative: the role of technology to unveil the potential of a novel tropical biodiversity-based economy. Land use. Assessing the Past, Envisioning the Future.
Ozercan, H. I., Ileri, A. M., Ayday, E., and Alkan, C. (2018). Realizing the potential of blockchain technologies in genomics. Genome research, 28(9):1255–1263.
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Seppey, M., Manni, M., and Zdobnov, E. M. (2019). BUSCO: Assessing Genome Assembly and Annotation Completeness, pages 227–245. Springer, New York, NY.
Shiraishi, F., Perles, V., Yassuda, H., Kimura, L., Andrade, E., and Simplicio, M. (2021). Torrente, a micropayment based Bittorrent extension to mitigate free riding. In Proc. of the XXI Brazilian Symposium on Information and Computational Systems Security (SBSeg), pages 82–89, Porto Alegre/RS, Brazil. SBC.
SisGen (2021). Sisgen - sistema nacional de gestão de patrimônio genético e do conhecimento tradicional associado. [link]. [On-line; accessed 23-February-2021].
Strand, J., Soares-Filho, B., Costa, M. H., Oliveira, U., Ribeiro, S. C., Pires, G. F., Oliveira, A., Rajão, R., May, P., van der Hoff, R., Siikamaki, J., da Motta, R. S., and Toman, M. (2018). Spatially explicit valuation of the Brazilian Amazon forest’s ecosystem services. Nature Sustainability, 1(11):657–664.
UNDP (2021). A pilot to improve genetic resources traceability through blockchain technology launched by the UNDP GEF Global ABS project. [link]. Acessed on 29-06-2021.
Beyene, M., Toussaint, P. A., Thiebes, S., Schlesner, M., Brors, B., and Sunyaev, A. (2022). A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research. Journal of the American Medical Informatics Association, 29(8):1433–1444.
Boscarioli, C., de Araujo, R. M., and Maciel, R. S. P. (2017). I GranDSI-BR Grand Research Challenges in Information Systems in Brazil 2016-2026.
Buck, M. and Hamilton, C. (2011). The Nagoya protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their utilization to the convention on biological diversity. Review of ECIEL, 20(1):47–61.
Carlini, R., Carlini, F., Dalla Palma, S., and Pareschi, R. (2019). Genesy: a blockchain-based platform for DNA sequencing. DLT@ ITASEC, 2019:68–72.
Cohen, B. (2003). Incentives build robustness in BitTorrent. In Workshop on Economics of Peer-to-Peer systems, volume 6, pages 68–72.
Encrypgen (2017). The clinical and investment potential in the gene-chain project the unprecedented growth of genomic data.
Gilman, E. and Barth, D. (2017). Zero Trust Networks. O’Reilly Media, Incorporated.
Glowka, L., Burhenne-Guilmin, F., Synge, H., McNeely, J. A., and G ̈undling, L. (1994). A guide to the convention on biological diversity.
Grishin, D., Obbad, K., Estep, P., Cifric, M., Zhao, Y., and Church, G. (2018). Blockchain-enabled genomic data sharing and analysis platform. Technical report, Nebula Genomics.
Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A., Anderson, C. L., Figueiredo, J. P., Jaramillo, C., Riff, D., Negri, F. R., Hooghiemstra, H., Lundberg, J., Stadler, T., Särkinen, T., and Antonelli, A. (2010). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science, 330(6006):927–931.
Ito, K. and O’Dair, M. (2019). A critical examination of the application of blockchain technology to intellectual property management. In Business transformation through blockchain, pages 317–335. Springer.
Kimura, L., Andrade, E., Carvalho, T., and Junior, M. S. (2021). Amazon biobank - a community-based genetic database. In Proc. of the XXI SBSeg, pages 74–81, Porto Alegre/RS, Brazil. SBC.
Kimura, L. T., Andrade, E. R., Nobre, I., Nobre, C. A., de Medeiros, B. A. S., Riaño-Pachón, D. M., Shiraishi, F. K., Carvalho, T. C. M. B., and Simplicio, M. A. (2023). Amazon biobank: a collaborative genetic database for bioeconomy development. Functional & Integrative Genomics, 23(2):101.
Kulemin, N., Popov, S., and Gorbachev, A. (2017). The zenome project: Whitepaper blockchain-based genomic ecosystem. Zenome. io, page A.
Li, F.-W. (2021). Decolonizing botanical genomics. Nature Plants, 7(12):1542–1543.
Mgbeoji, I. (2007). Global biopiracy: patents, plants, and indigenous knowledge. ubc Press.
Nobre, C. A., Sampaio, G., Borma, L. S., Castilla-Rubio, J. C., Silva, J. S., and Cardoso, M. (2016). Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm. Proc. of the National Academy of Sciences, 113(39):10759–10768.
Nobre, I. and Nobre, C. A. (2019). The Amazonia third way initiative: the role of technology to unveil the potential of a novel tropical biodiversity-based economy. Land use. Assessing the Past, Envisioning the Future.
Ozercan, H. I., Ileri, A. M., Ayday, E., and Alkan, C. (2018). Realizing the potential of blockchain technologies in genomics. Genome research, 28(9):1255–1263.
Rech, E. (2011). Genomics and synthetic biology as a viable option to intensify sustainable use of biodiversity. Nature Precedings.
Seppey, M., Manni, M., and Zdobnov, E. M. (2019). BUSCO: Assessing Genome Assembly and Annotation Completeness, pages 227–245. Springer, New York, NY.
Shiraishi, F., Perles, V., Yassuda, H., Kimura, L., Andrade, E., and Simplicio, M. (2021). Torrente, a micropayment based Bittorrent extension to mitigate free riding. In Proc. of the XXI Brazilian Symposium on Information and Computational Systems Security (SBSeg), pages 82–89, Porto Alegre/RS, Brazil. SBC.
SisGen (2021). Sisgen - sistema nacional de gestão de patrimônio genético e do conhecimento tradicional associado. [link]. [On-line; accessed 23-February-2021].
Strand, J., Soares-Filho, B., Costa, M. H., Oliveira, U., Ribeiro, S. C., Pires, G. F., Oliveira, A., Rajão, R., May, P., van der Hoff, R., Siikamaki, J., da Motta, R. S., and Toman, M. (2018). Spatially explicit valuation of the Brazilian Amazon forest’s ecosystem services. Nature Sustainability, 1(11):657–664.
UNDP (2021). A pilot to improve genetic resources traceability through blockchain technology launched by the UNDP GEF Global ABS project. [link]. Acessed on 29-06-2021.
Publicado
20/05/2024
Como Citar
KIMURA, Leonardo T.; SIMPLÍCIO JR, Marcos A..
Amazon Biobank: a Blockchain-based Genomic Database for Bioeconomy. In: CONCURSO DE TESES E DISSERTAÇÕES EM SISTEMAS DE INFORMAÇÃO - SIMPÓSIO BRASILEIRO DE SISTEMAS DE INFORMAÇÃO (SBSI), 20. , 2024, Juiz de Fora/MG.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2024
.
p. 86-101.
DOI: https://doi.org/10.5753/sbsi_estendido.2024.238604.
