22 papers · ranked by Valyu relevance
Peter Sestoft
Research relies on ever larger amounts of data from experiments, automated production equipment, questionnaries, times series such as weather records, and so on. A major task in science is to combine, process and analyse such data to obtain evidence of patterns and correlations. Most research data are on digital form…
Halima Samra, Alice Li, Ben Soh
Current health information systems used in genetic research centers and clinics in the Kingdom of Saudi Arabia have failed to enable researchers and health care physicians to utilize genetic and clinical data in their research. In this paper, we aim to design and implement a Genetic Disorders Diagnosis Data Management…
Qin Wang, Youhuan Li, Yansong Feng, Si Chen + 11 more
'Zhichao Shi' 'Yuequn Dou' 'chuchu Gao' 'Zebin Huang' 'Zihui Si' 'Yixuan Chen' 'Zhaohai Sun' 'Ke Tang' 'Wenqiang Jin'] The relational database design would output a schema based on user's requirements, which defines table structures and their interrelated relations. Translating requirements into accurate schema…
Jacob Anhøj, Prakash Nadkarni
Background The complexity and the rapid evolution and expansion of the domain of clinical information make development and maintenance of clinical databases difficult. Whenever new data types are introduced or existing types are modified in a conventional relational database system, the physical design of the database…
Dimitri Yatsenko, Edgar Y. Walker, Andreas S. Tolias
The relational data model offers unrivaled rigor and precision in defining data structure and querying complex data. Yet the use of relational databases in scientific data pipelines is limited due to their perceived unwieldiness. We propose a simplified and conceptually refined relational data model named DataJoint.…
Sherri Weitl-Harms
This paper describes a service learning project used in an upper-level/graduate-level database systems course. Students complete a small database project for a real client. The final product must match the client specification and needs, and include the database design and the final working database system with…
Dimitri Yatsenko, Jacob Reimer, Alexander S. Ecker, Edgar Y. Walker + 6 more
The rise of big data in modern research poses serious challenges for data management: Large and intricate datasets from diverse instrumentation must be precisely aligned, annotated, and processed in a variety of ways to extract new insights. While high levels of data integrity are expected, research teams have diverse…
Malcolm Crowe, Fritz Laux
– This paper reviews suggestions for changes to database technology coming from the work of many researchers, particularly those working with evolving big data. We discuss new approaches to remote data access and standards that better provide for durability and auditability in settings including business and scientific…
Baldeep Singh, Randall Martyr, Thomas Medland, Jamie Astin + 2 more
'Gordon Hunter' 'Jean-Christophe Nebel'] About fifty years ago, the world’s first fully automated system for trading securities was introduced by Instinet in the US. Since then the world of trading has been revolutionised by the introduction of electronic markets and automatic order execution. Nowadays, financial…
Authors not listed
Mass spectrometry (MS) generates large datasets that are stored in increasingly optimized and complex file types, demanding technical expertise to extract information rapidly and easily. We wondered whether a simple structured query language (SQL) database could hold raw MS data and allow for easily readable queries…
Mohamed Hassan
In the world of data management, the rapidly growing area of big data offers both intriguing possibilities and substantial obstacles. Big data, defined by its enormous size, complex structure, and varied sources - which include everything from social media engagement and sensor data to financial transactions and…
Michael Statt, Kristopher Brown, Santosh Suram, Linda Hung + 3 more
In this work, we present DBgen, a Python library that provides a framework for defining extract-transform-load (ETL) pipelines to create and populate SQL databases. DBgen is most useful when the underlying data has complex relationships, requires multi-step analysis, is large-scale, and the type of data being collected…
Junseok Park, Kwangmin Kim, Seongkuk Park, Woochang Hwang + 3 more
A clinical trial protocol defines the procedural methods that should be performed during a clinical trial. Every clinical trial starts with the design of its protocol. In designing the protocol, it is common for researchers to refer to electronic databases and extract protocol elements from clinical trial information…
Moisés Silva-Muñoz, Alberto Franzin, Hugues Bersini, Muhammad Aleem
Database systems play a central role in modern data-centered applications. Their performance is thus a key factor in the efficiency of data processing pipelines. Modern database systems expose several parameters that users and database administrators can configure to tailor the database settings to the specific…
Jasper Kyle Catapang
Databases play an essential role in our society today. Databases are embedded in sectors like corporations, institutions, and government organizations, among others. These databases are used for our video and audio streaming platforms, social gaming, finances, cloud storage, e-commerce, healthcare, economy, etc. It is…
Marta Chronowska, Michael J. Stam, Derek N. Woolfson, Luigi F. Di Constanzo + 1 more
The field of protein design has changed dramatically over the last 40 years, with a range of methods developing from rational design to more recent data-driven approaches. While considerable insight could be gained from analysing designed proteins, there is no single resource that brings together all the relevant data…
Clark C. Evans, Kyrylo Simonov
A new way to conceptualize computations, Query Combinators, can be used to create a data processing environment shared among the entire medical research team. For a given research context, a domain specific query language can be created that represents data sources, analysis methods, and integrative domain knowlege.…
Michael Statt, Brian Rohr, Dan Guevarra, Ja'Nya Breeden + 2 more
Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical…
Guillermo Yáñez Feliú, Benjamín Earle Gómez, Verner Codoceo Berrocal, Macarena Muñoz Silva + 8 more
Characterization is fundamental to the design, build, test, learn (DBTL) cycle for engineering synthetic genetic circuits. Components must be described in such a way as to account for their behavior in a range of contexts. Measurements and associated metadata, including part composition, constitute the test phase of…
José J. Naveja-Romero, Fernanda I. Saldívar-González, Diana L. Prado-Romero, Angel J. Ruiz-Moreno + 3 more
The manuscript discusses recent advances on computer-aided drug discovery (CADD) with focus on data-dependent drug discovery. Herein, we do not intend to review the many CADD methodologies comprehensively. Instead, the review discusses progress on selected concepts, methodologies, resources, and applications that are…
Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche + 3 more
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry…
Diana L. Prado-Romero, Fernanda I. Saldívar-González, Iván López-Mata, Pedro A. Laurel-García + 2 more
Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy used in combination with…