Efficient logging and querying for blockchain-based cross-site genomic dataset access audit

• Type of Material: Article
• Authors: Shuaicheng Ma, Emory University; Yang Cao, Kyoto University; Li Xiong, Emory University
• Language: English
• Date: 2020-07-21
• Publisher: BMC
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s).
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s12920-020-0725-y
• Title of Journal or Parent Work: BMC Medical Genomics
• Volume: 13
• Issue: Suppl 7
• Start Page: 91
• End Page: 91
• Grant/Funding Information: NSF under grant CNS-1618932, the AFOSR DDDAS program under grant FA9550-121-0240,; This work was supported by NIH R01GM118609, Georgia CTSA under grant NIH UL1TR002378,; Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research No. 17H06099, No. 18H04093 and No. 19K20269.; The publication costs were funded by NIH R01GM118609, Georgia CTSA under grant NIH UL1TR002378, Japan Society for the Promotion of Science (JSPS) No. 17H06099, No. 18H04093, No. 19K20269.
• Keywords: Blockchain; Genome; Life Sciences & Biomedicine; Cross-site genomic datasets; Genetics & Heredity; Access log audit; Privacy; Science & Technology

Abstract

Background Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module plays an essential role in ensuring the accountability. A centralized access log audit system is vulnerable to the single point of attack and also lack transparency since the log could be tampered by a malicious system administrator or internal adversaries. Several studies have proposed blockchain-based access audit to solve this problem but without considering the efficiency of the audit queries. The 2018 iDASH competition first track provides us with an opportunity to design efficient logging and querying system for cross-site genomic dataset access audit. We designed a blockchain-based log system which can provide a light-weight and widely compatible module for existing blockchain platforms. The submitted solution won the third place of the competition. In this paper, we report the technical details in our system. Methods We present two methods: baseline method and enhanced method. We started with the baseline method and then adjusted our implementation based on the competition evaluation criteria and characteristics of the log system. To overcome obstacles of indexing on the immutable Blockchain system, we designed a hierarchical timestamp structure which supports efficient range queries on the timestamp field. Results We implemented our methods in Python3, tested the scalability, and compared the performance using the test data supplied by competition organizer. We successfully boosted the log retrieval speed for complex AND queries that contain multiple predicates. For the range query, we boosted the speed for at least one order of magnitude. The storage usage is reduced by 25%. Conclusion We demonstrate that Blockchain can be used to build a time and space efficient log and query genomic dataset audit trail. Therefore, it provides a promising solution for sharing genomic data with accountability requirement across multiple sites.