24 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…
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…
Rebekah Duke, Vinayak Bhat, Chad Risko
As buzzwords like “big data,” “machine learning,” and “high-throughput” expand through chemistry, chemists need to consider more than ever their data storage, data management, and data accessibility, whether in their own laboratories or with the broader community. While it is commonplace for chemists to use…
Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer + 2 more
'Adrian Viehweger' 'Christian Brandt'] Title: Abstract With the rapidly growing amount of biological data, powerful but also flexible data management and visualization systems are of increasingly crucial importance. The COVID-19 pandemic has more than highlighted this need and the challenges scientists are facing.…
Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta + 3 more
'David WJ Stringer-Calvert' 'Jessica D Tenenbaum' 'Peter D Karp'] Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational…
Aleem Akhtar
—Databases are considered to be integral part of modern information systems. Almost every web or mobile application uses some kind of database. Database management systems are considered to be a crucial element from both business and technological standpoint. This paper divides different types of database management…
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…
Paul L. Soto
Data collection and analysis are central to scientific research, including in applied and basic behavior analysis. A substantial amount of attention has been given to how to rigorously collect and analyze data. Less attention has been paid to storing and maintaining research data, which becomes a critical step in the…
Shahid Ullah, Wajeeha Rahman, Farhan Ullah, Gulzar Ahmad + 2 more
'Muhmmad Ijaz' 'Tianshun Gao'] Background: The achievement of the human genome project provides a basis for the systematic study of the human genome from evolutionary history to disease-specific medicine. With the explosive growth of biological data, a growing number of biological databases are being established to…
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…
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…
Niema Moshiri
In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics…
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…
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…
Authors not listed
In recent years, the development of large language models (LLMs) has revolutionized various fields of natural science, yet their application in molecular data processing remains constrained due to the reliance on single-modality inputs and outputs. To bridge the gap between experimenters and computational tools, we…
Amro F. Alasta, Muftah A. Enaba
—Since the use of computers in business world, data collection has become one of the most important issues due to the available knowledge in the data; such data has been stored in database. Database system was developed which led to the evolvement of hierarchical and relational database followed by Standard Query…
Dhanamma Jagli, Priyanka Gaikwad, Shubhangi Gunjal, Chaitanya Bilaware
'Chaitanya Bilaware'] Abstract. This paper describes practical observations during the Database system Lab. Oracle 10g DBMS is used in the data base system lab and performed SQL queries based many concepts like Data Definition Language Commands (DDL), Data Modification Language Commands ((DML), Views, Integrity…
Chaimae Asaad, Karim Bäına, Mounir Ghogho
The demanding requirements of the new Big Data intensive era raised the need for flexible storage systems capable of handling huge volumes of unstructured data and of tackling the challenges that traditional databases were facing. NoSQL Databases, in their heterogeneity, are a powerful and diverse set of databases…
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…
Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel
We investigate and analyse the data quality of nucleotide sequence databases with the objective of automatic detection of data anomalies and suspicious records. Specifically, we demonstrate that the published literature associated with each data record can be used to automatically evaluate its quality, by…
Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan + 10 more
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl “Core” database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome…
Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner + 6 more
Open biological data is distributed over many resources making it challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate…
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…
Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good + 20 more
Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe the breadth and depth of biomedical knowledge contained within Wikidata, assembled from primary knowledge repositories on genomics, proteomics…