Dataset Information

Decentralized genomics audit logging via permissioned blockchain ledgering.

ABSTRACT: BACKGROUND:One of the tasks in the iDASH Secure Genome Analysis Competition in 2018 was to develop blockchain-based immutable logging and querying for a cross-site genomic dataset access audit trail. The specific challenge was to design a time/space efficient structure and mechanism of storing/retrieving genomic data access logs, based on MultiChain version 1.0.4 ( https://www.multichain.com/ ). METHODS:Our technique uses the MultiChain stream application programming interface (which affords treating MultiChain as a key value store) and employs a two-level index, which naturally supports efficient queries of the data for single clause constraints. The scheme also supports heuristic and binary search techniques for queries containing conjunctions of clause constraints, and timestamp range queries. Of note, all of our techniques have complexity independent of inserted data set size, other than the timestamp ranges, which logarithmically scale with input size. RESULTS:We implemented our insertion and querying techniques in Python, using the MultiChain library Savoir ( https://github.com/dxmarkets/savoir ), and comprehensively tested our implementation across a benchmark of datasets of varying sizes. We also tested a port of our challenge submission to a newer version of MultiChain (2.0 beta), which natively supports multiple indices. CONCLUSIONS:We presented creative and efficient techniques for storing and querying log file data in MultiChain 1.0.4 and 2.0 beta. We demonstrated that it is feasible to use a permissioned blockchain ledger for genomic query log data when data volume is on the order of hundreds of megabytes and query times of dozens of minutes is acceptable. We demonstrated that evolution in the ledger platform (MultiChain 1 to 2) yielded a 30%-40% increase in insertion efficiency. All source code for this challenge has been made available under a BSD-3 license from https://github.com/sandialabs/idash2018task1/ .

SUBMITTER: Pattengale ND

PROVIDER: S-EPMC7372871 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Decentralized genomics audit logging via permissioned blockchain ledgering.

Pattengale Nicholas D ND Hudson Corey M CM

BMC medical genomics 20200721 Suppl 7

<h4>Background</h4>One of the tasks in the iDASH Secure Genome Analysis Competition in 2018 was to develop blockchain-based immutable logging and querying for a cross-site genomic dataset access audit trail. The specific challenge was to design a time/space efficient structure and mechanism of storing/retrieving genomic data access logs, based on MultiChain version 1.0.4 ( https://www.multichain.com/ ).<h4>Methods</h4>Our technique uses the MultiChain stream application programming interface (wh ...[more]

PMID: 32693795

Similar Datasets

Project description: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.

Project description:BACKGROUND:As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storage and sharing is Ethereum smart contracts. Ethereum is a blockchain platform, and smart contracts are immutable pieces of code running on virtual machines in this platform that can be invoked by a user or another contract (in the blockchain network). The 2019 iDASH (Integrating Data for Analysis, Anonymization, and Sharing) competition for Secure Genome Analysis challenged participants to develop time- and space-efficient Ethereum smart contracts for gene-drug relationship data. METHODS:Here we design a specific smart contract to store and query gene-drug interactions in Ethereum using an index-based, multi-mapping approach. Our contract stores each pharmacogenomics observation, a gene-variant-drug triplet with outcome, in a mapping searchable by a unique identifier, allowing for time and space efficient storage and query. This solution ranked in the top three at the 2019 IDASH competition. We further improve our "challenge solution" and develop an alternate "fastQuery" smart contract, which combines together identical gene-variant-drug combinations into a single storage entry, leading to significantly better scalability and query efficiency. RESULTS:On a private, proof-of-authority network, both our challenge and fastQuery solutions exhibit approximately linear memory and time usage for inserting into and querying small databases (<1,000 entries). For larger databases (1000 to 10,000 entries), fastQuery maintains this scaling. Furthermore, both solutions can query by a single field ("0-AND") or a combination of fields ("1- or 2-AND"). Specifically, the challenge solution can complete a 2-AND query from a small database (100 entries) in 35ms using 0.1 MB of memory. For the same query, fastQuery has a 2-fold improvement in time and a 10-fold improvement in memory. CONCLUSION:We show that pharmacogenomics data can be stored and queried efficiently using Ethereum blockchain. Our solutions could potentially be used to store a range of clinical data and extended to other fields requiring high-integrity data storage and efficient access.

Project description:BackgroundBlockchain technology has the potential to enable more secure, transparent, and equitable data management. In the health care domain, it has been applied most frequently to electronic health records. In addition to securely managing data, blockchain has significant advantages in distributing data access, control, and ownership to end users. Due to this attribute, among others, the use of blockchain to power personal health records (PHRs) is especially appealing.ObjectiveThis review aims to examine the current landscape, design choices, limitations, and future directions of blockchain-based PHRs.MethodsAdopting the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines, a cross-disciplinary systematic review was performed in July 2020 on all eligible articles, including gray literature, from the following 8 databases: ACM, IEEE Xplore, MEDLINE, ScienceDirect, Scopus, SpringerLink, Web of Science, and Google Scholar. Three reviewers independently performed a full-text review and data abstraction using a standardized data collection form.ResultsA total of 58 articles met the inclusion criteria. In the review, we found that the blockchain PHR space has matured over the past 5 years, from purely conceptual ideas initially to an increasing trend of publications describing prototypes and even implementations. Although the eventual application of blockchain in PHRs is intended for the health care industry, the majority of the articles were found in engineering or computer science publications. Among the blockchain PHRs described, permissioned blockchains and off-chain storage were the most common design choices. Although 18 articles described a tethered blockchain PHR, all of them were at the conceptual stage.ConclusionsThis review revealed that although research interest in blockchain PHRs is increasing and that the space is maturing, this technology is still largely in the conceptual stage. Being the first systematic review on blockchain PHRs, this review should serve as a basis for future reviews to track the development of the space.

Dataset Information

Decentralized genomics audit logging via permissioned blockchain ledgering.

Publications

Decentralized genomics audit logging via permissioned blockchain ledgering.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets