Hekaton Diaconu, Cristian; Freedman, Craig; Ismert, Erik ...
Proceedings of the 2013 ACM SIGMOD International Conference on Management of Data,
06/2013
Conference Proceeding
Hekaton is a new database engine optimized for memory resident data and OLTP workloads. Hekaton is fully integrated into SQL Server; it is not a separate system. To take advantage of Hekaton, a user ...simply declares a table memory optimized. Hekaton tables are fully transactional and durable and accessed using T-SQL in the same way as regular SQL Server tables. A query can reference both Hekaton tables and regular tables and a transaction can update data in both types of tables. T-SQL stored procedures that reference only Hekaton tables can be compiled into machine code for further performance improvements. The engine is designed for high con-currency. To achieve this it uses only latch-free data structures and a new optimistic, multiversion concurrency control technique. This paper gives an overview of the design of the Hekaton engine and reports some experimental results.
We live in an increasingly interconnected world, with many organizations operating across countries or even continents. To serve their global user base, organizations are replacing their legacy DBMSs ...with cloud-based systems capable of scaling OLTP workloads to millions of users. CockroachDB is a scalable SQL DBMS that was built from the ground up to support these global OLTP workloads while maintaining high availability and strong consistency. Just like its namesake, CockroachDB is resilient to disasters through replication and automatic recovery mechanisms. This paper presents the design of CockroachDB and its novel transaction model that supports consistent geo-distributed transactions on commodity hardware. We describe how CockroachDB replicates and distributes data to achieve fault tolerance and high performance, as well as how its distributed SQL layer automatically scales with the size of the database cluster while providing the standard SQL interface that users expect. Finally, we present a comprehensive performance evaluation and share a couple of case studies of CockroachDB users. We conclude by describing lessons learned while building CockroachDB over the last five years.
Data is a valuable corporate asset and its effective management is vital to an organisation's success. This professional guide covers all the key areas of data management, including database ...development and corporate data modelling. It is business-focused, providing the knowledge and techniques required to successfully implement the data management function. This new edition adds chapters on linked data, concept systems and big data and artificial intelligence.
Retrieving the qualitative literature can be challenging, but the number and specific choice of databases are key factors. The aim of the present study is to provide guidance for the choice of ...databases for retrieving qualitative health research.
Seventy-one qualitative systematic reviews, from the Cochrane Database of Systematic Reviews and JBI database of Systematic Reviews and Implementation Reports, including 927 qualitative studies, were used to analyze the coverage of the qualitative literature in nine bibliographic databases.
The results show that 94.4% of the qualitative studies are indexed in at least one database, with a lower coverage for publication types other than journal articles. Maximum recall with two databases is 89.1%, with three databases recall increases to 92% and maximum recall with four databases is 93.1%. The remaining 6.9% of the publications consists of 1.3% scattered across five databases and 5.6% that are not indexed in any of the nine databases used in this study.
Retrieval in one or a few—although well selected—databases does not provide all the relevant qualitative studies. The remaining studies needs to be located using several other databases and alternative search strategies.
•94.4% of the included studies in qualitative reviews are indexed in at least one of the nine databases. Coverage is higher for journal articles.•Using four databases, it is possible to retrieve 93.1% of the publications.•Retrieval in one or a few databases does not provide all the relevant qualitative literature, and the remaining studies need to be located using several other databases and alternative search strategies.
KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database ...entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
Information Modeling and Relational Databases, Second Edition, provides an introduction to ORM (Object-Role Modeling)and much more. In fact, it is the only book to go beyond introductory coverage and ...provide all of the in-depth instruction you need to transform knowledge from domain experts into a sound database design. This book is intended for anyone with a stake in the accuracy and efficacy of databases: systems analysts, information modelers, database designers and administrators, and programmers. Terry Halpin, a pioneer in the development of ORM, blends conceptual information with practical instruction that will let you begin using ORM effectively as soon as possible. Supported by examples, exercises, and useful background information, his step-by-step approach teaches you to develop a natural-language-based ORM model, and then, where needed, abstract ER and UML models from it. This book will quickly make you proficient in the modeling technique that is proving vital to the development of accurate and efficient databases that best meet real business objectives. * Presents the most indepth coverage of Object-Role Modeling available anywhere, including a thorough update of the book for ORM2, as well as UML2 and E-R (Entity-Relationship) modeling * Includes clear coverage of relational database concepts, and the latest developments in SQL and XML, including a new chapter on the impact of XML on information modeling, exchange and transformation * New and improved case studies and exercises are provided for many topics
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and ...industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.
Abstract
The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, ...diseases, and exposures to advance understanding about human health. Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions. In this biennial update, we report a 20% increase in CTD curated content and now provide 45 million toxicogenomic relationships for over 16 300 chemicals, 51 300 genes, 5500 phenotypes, 7200 diseases and 163 000 exposure events, from 600 comparative species. Furthermore, we increase the functionality of chemical–phenotype content with new data-tabs on CTD Disease pages (to help fill in knowledge gaps for environmental health) and new phenotype search parameters (for Batch Query and Venn analysis tools). As well, we introduce new CTD Anatomy pages that allow users to uniquely explore and analyze chemical–phenotype interactions from an anatomical perspective. Finally, we have enhanced CTD Chemical pages with new literature-based chemical synonyms (to improve querying) and added 1600 amino acid-based compounds (to increase chemical landscape). Together, these updates continue to augment CTD as a powerful resource for generating testable hypotheses about the etiologies and molecular mechanisms underlying environmentally influenced diseases.
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