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Benchmarking distributed data warehouse solutions for storing genomic variant information

Marek S. Wiewiórka, Dawid P. Wysakowicz, Michał J. Okoniewski, Tomasz Gambin
2017 Database: The Journal of Biological Databases and Curation  
Next, we have benchmarked performance of a number of combinations of distributed storages and query engines on a set of SQL queries that address biological questions essential for both research and medical  ...  At a time when thousands of patientss sequenced exomes and genomes are becoming available, there is a growing need for efficient database storage and querying.  ...  Supplementary data Conflict of interest. None declared.  ... 
doi:10.1093/database/bax049 pmid:29220442 pmcid:PMC5504537 fatcat:hgwwc2buifbjfj5i77jrxeh6xi

Genomic and Proteomic Databases: Foundations, Current Status and Future Applications

Shamkant B. Navathe, Upen Patil, Wei Guan
2007 Journal of Computing Science and Engineering  
Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among  ...  Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are  ...  ACKNOWLEDGMENTS The authors are grateful for the contributions of Ying Liu, Saurav Sahay and Neha Narkhede during the development of this paper. The anonymous referees also provided useful comments.  ... 
doi:10.5626/jcse.2007.1.1.001 fatcat:sawebfga3bfybdibfq3yvhjf5u

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

Saikat Chowdhury, Ram Rup Sarkar
2015 Database: The Journal of Biological Databases and Curation  
perform a thorough review on popular and actively functioning 24 cell signaling databases.  ...  To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate  ...  Conflict of interest: None declared.  ... 
doi:10.1093/database/bau126 pmid:25632107 pmcid:PMC4309023 fatcat:b6y4vbdg7rfdrac5z3htaxdcji

Big Data and Data-Driven Healthcare Systems

Cheryl Ann Alexander, Lidong Wang
2018 Journal of Business and Management Sciences  
Big data and Big Data analytics in healthcare systems are presented in this paper. Information security, privacy, and challenges of Big Data analytics in healthcare are also discussed.  ...  Traditional data management techniques are often unable to manage the voluminous amounts of data produced in healthcare systems.  ...  Fast statistical and analysis platform of medical service big data should provide the following functions: the design of new data structure in the distributed database(HBase) which is capable for processing  ... 
doi:10.12691/jbms-6-3-7 fatcat:dkq67ndconhktpvjhf4gkbtqey

Migrating a research data warehouse to a public cloud: challenges and opportunities

Michael G Kahn, Joyce Y Mui, Michael J Ames, Anoop K Yamsani, Nikita Pozdeyev, Nicholas Rafaels, Ian M Brooks
2021 JAMIA Journal of the American Medical Informatics Association  
New RDWs are migrating to cloud platforms for the scalability and flexibility needed to meet these challenges. We describe our experience in migrating a multi-institutional RDW to a public cloud.  ...  The computing and storage needs of these research environments may quickly exceed the capacity of on-premises systems.  ...  Compass as a data steward of fully identified patient clinical and genomic data.  ... 
doi:10.1093/jamia/ocab278 pmid:34919694 pmcid:PMC8922165 fatcat:d4xflguhyvbmze2necxfmzpmsa

In Search of Big Medical Data Integration Solutions -A Comprehensive Survey

Houssein Dhayne, Rafiqul Haque, Rima Kilany, Yehia Taher
2019 IEEE Access  
For instance, the healthcare sector is confronting difficulties in respect of integration or fusion of diverse medical data stemming from multiple heterogeneous sources.  ...  In recent years, the radical advancement of technologies has given rise to an abundance of software applications, social media, and smart devices such as smartphone, sensors, and so on.  ...  These solutions often depend on different data dimensions as well as the type of data and the target to be studied. B.  ... 
doi:10.1109/access.2019.2927491 fatcat:6ooixehrznfdnbwghzfeds3mky

Report from the 3rd Workshop on Extremely Large Databases

Jacek Becla, Kian-Tat Lim, Daniel Liwei Wang
2010 Data Science Journal  
Applying for funding from the European Commission for Europe-based XLDB and/or SciDB activities through "FP7" proposals will be considered.  ...  Several solution providers presented their thoughts on terascale and petascale analytics. MonetDB presented a successful port of the SDSS multi-terabyte database.  ...  However, while the RDBMS model operates on sets, MR functions operate on a single pair at a time. The latter was thought to be more approachable for end users.  ... 
doi:10.2481/dsj.xldb09 fatcat:574dpairjbb6zh2l5qywipgm4m

A Meta Data Vault Approach for Evolutionary Integration of Big Data Sets : Case Study Using the NCBI Database for Genetic Variation

Zaineb Naamane, Vladan Jovanovic
2017 International Journal of Computer Science & Information Technology (IJCSIT)  
A data warehouse integrates data from various and heterogeneous data sources and creates a consolidated view of the data that is optimized for reporting and analysis.  ...  To test the proposed model, we have used big data sets from the biomedical field and for each modification of the data source schema, we outline the changes that need to be made to the EDW, the data marts  ...  The rs identifier represents aggregation by type of sequence change and location on the genome if an assembled genome is available, or aggregation by common sequence if a genome is not available (Kitts  ... 
doi:10.5121/ijcsit.2017.9307 fatcat:4tsespm53jdyljpbp77imsgrj4

Methods and Trends in Information Retrieval in Big Data Genomic Research

There was a surge of genomic information from the different literature and the production of genome datasets that catapulted the development of several tools for analyzing and presenting new found knowledge  ...  This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  There was a rapid expansion of the cancer genome data sets also accelerated the genetic analytical tools for genome association studies and analysis through microarray.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Visualizing the Protein Sequence Universe

Larissa Stanberry, Roger Higdon, Winston Haynes, Natali Kolker, William Broomall, Saliya Ekanayake, Adam Hughes, Yang Ruan, Judy Qiu, Eugene Kolker, Geoffrey Fox
2013 Concurrency and Computation  
Existing resources lack scalable visualization tools that are instrumental for functional annotation.  ...  The advantages of the method and its implementation include the ability to scale to large numbers of sequences, integrate different similarity measures with other functional and experimental data, and  ...  INTRODUCTION Functional annotation of newly sequenced genomes and meta-genomes is one of the principal challenges of modern biology.  ... 
doi:10.1002/cpe.3072 fatcat:2wquzyqrxjgg5crnjhzvrqmkru

Visualizing the protein sequence universe

Larissa Stanberry, Eugene Kolker, Geoffrey Fox, Roger Higdon, Winston Haynes, Natali Kolker, William Broomall, Saliya Ekanayake, Adam Hughes, Yang Ruan, Judy Qiu
2012 Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences - ECMLS '12  
The advantages of the proposed PSU method include the ability to scale to large numbers of sequences, integrate different similarity measures with other functional and experimental data, and facilitate  ...  Existing resources lack scalable visualization tools that are instrumental for functional annotation.  ...  We are greatful to Elizabeth Stewart and Christopher Moss for critical reading of the paper and insightful discussions.  ... 
doi:10.1145/2483954.2483958 fatcat:4bwfbqq6tjgchcydva7qi3s7d4

Information engineering infrastructure for life sciences and its implementation in China

WeiMin Zhu, YunPing Zhu, XiaoLing Yang
2013 Science China Life Sciences  
The demand for such power in omics studies is argued as the fundamental function to meet for CIEIPOS.  ...  Implementation outlook of CIEIPOS in hardware and network is discussed. biological database services, omics informatics, information engineering infrastructure for pan-omics studies Citation: Zhu W M,  ...  Its Hotdata database aggregates supplementary datasets of journal articles, providing biologists with a unique data resource.  ... 
doi:10.1007/s11427-013-4440-1 pmid:23526387 fatcat:mxamluxjdzbnfdgjdwncvixyxe

Welcome Message from the General Chair

2006 International Conference on Dependable Systems and Networks (DSN'06)  
The conference was a huge success for its time, attracting almost 100 papers and more than 150 participants. We have come a long way since then!  ...  Thanks to the efforts of programme committees, authors, and the VLDB Endowment over the years, VLDB conferences constitute today a prestigious scientific forum for the presentation and exchange of research  ...  compiled similar guides for ICSE 2001 and RE 2001, respectively  ... 
doi:10.1109/dsn.2006.75 dblp:conf/dsn/X06 fatcat:k4duddvbk5glboxkqxkkfsh4p4

RSECM: Robust Search Engine using Context-based Mining for Educational Big Data

D. Pratiba, G. Shobha
2016 International Journal of Advanced Computer Science and Applications  
With an accelerating growth in the educational sector along with the aid of ICT and cloud-based services, there is a consistent rise of educational big data, where storage and processing become the prime  ...  Hence, there is less applicability of mining techniques for upcoming search engine due to unstructured educational data. The proposed system introduces a technique called as RSECM i.e.  ...  [11] , where medical image analysis, physiological signal processing, and genomics data processing is discussed.  ... 
doi:10.14569/ijacsa.2016.071206 fatcat:vjidtmgrnbajrpsvhprdlkkxx4

Intel "big data" science and technology center vision and execution plan

Michael Stonebraker, Sam Madden, Pradeep Dubey
2013 SIGMOD record  
Intel held a national competition for a 5th Science and Technology center in 2012 and selected a proposal from M.I.T. with a theme of "Big Data".  ...  This paper presents the big data vision of this technology center and the execution plan for the first few years.  ...  The requirement is a scalable visualization system connected to a scalable database holding many terabytes of MODIS data. Problem 2: Medical records and ICU data.  ... 
doi:10.1145/2481528.2481537 fatcat:cfufdakydbfkfdjk2yftm572la
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