24 papers · ranked by Valyu relevance
Ali Ben Ammar
Graph databases (GDB) have recently been arisen to overcome the limits of traditional databases for storing and managing data with graph-like structure. Today, they represent a requirementfor many applications that manage graph-like data,like social networks.Most of the techniques, applied to optimize queries in graph…
Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
Over the past couple of decades, the explosion of densely interconnected data has stimulated the research, development and adoption of graph database technologies. From early graph models to more recent native graph databases, the landscape of implementations has evolved to cover enterprise-ready requirements. Because…
Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth + 3 more
'David Broneske' 'Gunter Saake' 'Robert Heyer'] Title: Abstract The increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving…
Christian Theil Have, Lars Juhl Jensen
Contact:Lars.Juhl.Jensen@gmail.com
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark + 2 more
Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and…
Renzo Angles, Claudio Gutiérrez
A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graphoriented operations and type constructors. In this article we present the basic notions of graph databases, give an…
Jens Schrodt, Aleksei Dudchenko, Petra Knaup-Gregori, Matthias Ganzinger
'Matthias Ganzinger'] Graph theory is a well-established theory with many methods used in mathematics to study graph structures. In the field of medicine, electronic health records (EHR) are commonly used to store and analyze patient data. Consequently, it seems straight-forward to perform research on modeling EHR data…
Chenwei Yan, Xinyue Fang, Xiaotong Huang, Chenyi Guo + 1 more
The knowledge graph is one of the essential infrastructures of artificial intelligence. It is a challenge for knowledge engineering to construct a high-quality domain knowledge graph for multi-source heterogeneous data. We propose a complete process framework for constructing a knowledge graph that combines structured…
Domagoj Vrgoč, Carlos Rojas, Renzo Angles, Marcelo Arenas + 6 more
'Diego Arroyuelo' 'Carlos Buil Aranda' 'Aidan Hogan' 'Gonzalo Navarro' 'Cristian Riveros' 'Juan Romero'] In this systems paper, we present MillenniumDB: a novel graph database engine that is modular, persistent, and open source. MillenniumDB is based on a graph data model, which we call domain graphs, that provides a…
Miguel E. Coimbra, Lucie Svitáková, Alexandre P. Francisco, Luís Veiga
'Luís Veiga'] Graph databases have become essential tools for managing complex and interconnected data, which is common in areas like social networks, bioinformatics, and recommendation systems. Unlike traditional relational databases, graph databases offer a more natural way to model and query intricate relationships…
Amine Ghrab, Oscar Romero, Sabri Skhiri, Alejandro Vaisman + 1 more
'Esteban Zimányi'] Abstract. Graph databases have emerged as the fundamental technology underpinning trendy application domains where traditional databases are not well-equipped to handle complex graph data. However, current graph databases support basic graph structures and integrity constraints with no standard…
Jero Schäfer, Ming Tang, Danny Luu, Anke Katharina Bergmann + 1 more
'Lena Wiese'] Background Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databases is challenging since these are often based on a relational schema and cannot be…
Adam Struck, Brian Walsh, Alexander Buchanan, Jordan A. Lee + 3 more
The analysis of cancer biology data involves extremely heterogeneous datasets including information from RNA sequencing, genome-wide copy number, DNA methylation data reporting on epigenomic regulation, somatic mutations from whole-exome or whole-genome analyses, pathology estimates from imaging sections or subtyping…
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…
Prashanth Athri, Vidhya Murali, Pradyumna Y Muralidhar, Cassandra Königs + 4 more
- 1. Department of Computer Science and Engineering, Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Bengaluru, India - 2. PES Center for Pattern Recognition, Department of Computer Science and Engineering, PES University, Bengaluru, India - 3. Bioinformatics and Medical Informatics, Bielefeld University…
Jordan K. Matelsky, Elizabeth P. Reilly, Erik C. Johnson, Jennifer Stiso + 3 more
Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These connectomics datasets continue to grow in size and complexity; methods to search for and identify interesting graph patterns offer a promising approach to quickly reduce data…
David Geleta, Andriy Nikolov, Gavin Edwards, Anna Gogleva + 10 more
The use of knowledge graphs as a data source for machine learning methods to solve complex problems in life sciences has rapidly become popular in recent years. Our Biological Insights Knowledge Graph (BIKG) combines relevant data for drug development from public as well as internal data sources to provide insights for…
Jianqiang Dong, Junwu Liu, Yifan Wei, Peilin Huang + 1 more
In biomedical research, the utilization of Knowledge Graph (KG) has proven valuable in gaining deep understanding of various processes. In this study, we constructed a comprehensive biomedical KG, named as MegaKG, by integrating a total of 23 primary data sources, which finally consisted of 188, 844 nodes/entities and…
Authors not listed
Background: Chemical reactions form intricate, highly connected networks whose exploration is essential for discovering more efficient and sustainable synthetic routes. As reaction data from literature, patents, and high‑throughput experimentation continue to surge, so does the need for tools that can collectively…
Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee + 5 more
Quantitative and qualitative data derived from the analysis of genomes, genes, proteins or metabolites from tissue or cells are currently generated in huge volumes during biomedical research. Graphia is an open-source platform created for the graph-based analysis of such complex data, e.g. transcriptomics, proteomics…
Marta Pasquini, Marco Stenta
Background. The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learning techniques support the development of new ways to extract value from the available reaction…
Roderic D. M. Page
Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in their own silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where…
Authors not listed
We present a unified, set–theoretic framework that extends molecular graphs to hypergraphs and superhypergraphs via iterated power sets. We define Molecular Graphs, Molecular HyperGraphs, and Molecular SuperHyperGraphs, and develop four complements over them: Weighted, Rough, Neural, and Multipolar frameworks. We prove…
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…