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Benchmarking distributed data warehouse solutions for storing genomic variant information
2017
Database: The Journal of Biological Databases and Curation
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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
2007
Journal of Computing Science and Engineering
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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
2015
Database: The Journal of Biological Databases and Curation
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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
2018
Journal of Business and Management Sciences
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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
2021
JAMIA Journal of the American Medical Informatics Association
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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
2019
IEEE Access
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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
2010
Data Science Journal
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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
2017
International Journal of Computer Science & Information Technology (IJCSIT)
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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
2019
VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE
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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
2013
Concurrency and Computation
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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
2012
Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences - ECMLS '12
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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
2013
Science China Life Sciences
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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)
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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
2016
International Journal of Advanced Computer Science and Applications
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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
2013
SIGMOD record
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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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