Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts.
Reads0
Chats0
TLDR
This work designs a specific smart contract to store and query gene-drug interactions in Ethereum using an index-based, multi-mapping approach, and develops 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.Abstract:
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. 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. 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. 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.read more
Citations
More filters
Journal ArticleDOI
A Review of Smart Contracts Applications in Various Industries: A Procurement Perspective
TL;DR: In this article, a mixed method of bibliometric analysis and systematic literature review is proposed to address the gap with a mixed-method of Bibliometric Analysis and systematic Literature Review.
Journal ArticleDOI
The Impact and Applications of Social Media Platforms for Public Health Responses Before and During the COVID-19 Pandemic: Systematic Literature Review
TL;DR: The positive and negative impact of social media platforms on public health are catalogued on the basis of recent research in this article , which is discussed in the context of improving future public health responses and incorporating other emerging digital technology domains such as artificial intelligence.
Journal ArticleDOI
A novel decentralized model for storing and sharing neuroimaging data using ethereum blockchain and the interplanetary file system
TL;DR: In this paper, the authors developed a proof-of-concept smart contract that stores patient brain tumor data such as patient identifier, disease, grade, chemotherapy drugs, and Karnofsky score.
Posted ContentDOI
Storing and analyzing a genome on a blockchain
TL;DR: A novel method of storing reference-aligned reads on-chain in a private blockchain network is developed and tools for accessing and analyzing the on- chain data are developed to provide open-source blockchain-based storage and access for advanced genomic analyses such as variant calling.
Journal ArticleDOI
Universal Wallets
Kim Peiter Jorgensen,Roman Beck +1 more
TL;DR: The focus in this paper is on universal wallets in blockchain systems, which can achieve the desired levels of security and stability.
References
More filters
PPCoin: Peer-to-Peer Crypto-Currency with Proof-of-Stake
Sunny King,Scott Nadal +1 more
TL;DR: Under this hybrid design proof-of-work mainly provides initial minting and is largely non-essential in the long run thus providing an energyefficient and more cost-competitive peer-to-peer crypto-currency.
Journal ArticleDOI
Blockchain distributed ledger technologies for biomedical and health care applications
TL;DR: This paper introduces blockchain technologies, including their benefits, pitfalls, and the latest applications, to the biomedical and health care domains and discusses the potential challenges and proposed solutions of adopting blockchain technologies in biomedical/health care domains.
Journal ArticleDOI
Routes for breaching and protecting genetic privacy.
Yaniv Erlich,Arvind Narayanan +1 more
TL;DR: An overview of genetic privacy breaching strategies is presented, outlining the principles of each technique, the underlying assumptions, and their technological complexity and maturation, as well as highlighting different cases that are relevant to genetic applications.
Book ChapterDOI
Performance and Scalability of Private Ethereum Blockchains
TL;DR: This work studies the effects of parameters on the performance of private smart contract platforms, which can be tailored by configuring blockchain-specific parameters like the time passing between two consecutive blocks, the size ofblocks, the hardware of the nodes running the blockchain software, or simply thesize of the network.
Journal ArticleDOI
Distributed E-Voting and E-Bidding Systems Based on Smart Contract
TL;DR: This study introduces the first decentralized electronic voting and bidding systems based on a blockchain and smart contract, which allow voters and bidders to participate in the opening phase and improve participant anonymity, the privacy of data transmission, and data reliability and verifiability.
Related Papers (5)
Effcient logging and querying for Blockchain-based cross-site genomic dataset access audit
Shuaicheng Ma,Yang Cao,Li Xiong +2 more
Efficient logging and querying for blockchain-based cross-site genomic dataset access audit
Shuaicheng Ma,Yang Cao,Li Xiong +2 more