Querying Graph Databases Research Articles

A logical approach to graph databases

Graph databases are now playing an important role because they allow us to overcome some limitations of relational databases. In particular, in graph databases we are interested not only on the data contained but also on its topology. As a consequence, most graph database queries are navigational, asking whether some nodes are connected by edges or paths.Up to now, most foundational work has concentrated on the study of computational models and query languages, analyzing their expressivity, computability, and complexity. However, in our work we address a different kind of foundational work. We are not concerned with expressibility, efficiency or feasibility issues, but with correctness. More precisely, given an algorithm or an implementation for solving queries, how can we be sure that the answers obtained are correct (soundness) and that all possible correct answers are obtained by our implementation (completeness).In this sense, in this paper we first present a core query language, similar to Cypher or G-Core. Then, we define a simple logic whose formulas are precisely the database queries, and whose satisfaction relation defines what is a correct answer. Finally, we define an operational semantics, which could be seen as an abstract implementation of our language, showing that the semantics is correct, i.e. sound and complete with respect to our logic.

Graph Theory Applications in Database Management

Graph theory, which is a branch of discrete mathematics, has emerged as a powerful tool in various domains, including database management. This abstract investigates the ways in which ideas and methods from graph theory which can be applied to database systems, offering a thorough synopsis of their benefits. Complex interactions within data can be well-modeled by using the basic concepts of graph theory, such as nodes, edges, and relationships. Because of its capacity to represent and query complex relationships, graph databases have become more and more popular in the field of database administration. Graph databases are well-suited for situations such as social networks, recommendation systems, and interconnected data domains because they are excellent at representing and traversing relationships, in contrast to standard relational databases, which are excellent at managing structured data. The abstract delves into the key graph-based data models, such as property graphs, RDF (Resource Description Framework), explaining how they facilitate the representation of diverse relationships. Furthermore, it explores the efficient storage and retrieval mechanisms that leverage graph traversal algorithms to extract valuable insights from interconnected datasets. The document highlights specific use cases where graph theory contributes to database management, including fraud detection, social network analysis, and recommendation systems. Additionally, it discusses the challenges associated with integrating graph databases into existing infrastructures and proposes solutions to address scalability and performance concerns. The abstract also touches upon the advancements in graph database query languages (Cypher) and SPARQL, showcasing their expressive power in querying complex relationships. The inclusion of graph-based indexing and optimization techniques demonstrates how database systems can efficiently handle queries involving large-scale graph data. As graph databases continue to evolve, this abstract concludes by outlining potential future directions in the intersection of graph theory and database management. It emphasizes the importance of ongoing research in developing scalable and efficient solutions for managing interconnected data, ultimately paving the way for more sophisticated and context-aware database systems relationships. Furthermore, it explores the efficient storage and retrieval mechanisms that leverage graph traversal algorithms to extract valuable insights from interconnected datasets.

Demystifying Graph Databases: Analysis and Taxonomy of Data Organization, System Designs, and Graph Queries

Numerous irregular graph datasets, for example social networks or web graphs, may contain even trillions of edges. Often, their structure changes over time and they have domain-specific rich data associated with vertices and edges. Graph database systems such as Neo4j enable storing, processing, and analyzing such large, evolving, and rich datasets. Due to the sheer size and irregularity of such datasets, these systems face unique design challenges. To facilitate the understanding of this emerging domain, we present the first survey and taxonomy of graph database systems. We focus on identifying and analyzing fundamental categories of these systems (e.g., document stores, tuple stores, native graph database systems, or object-oriented systems), the associated graph models (e.g., Resource Description Framework or Labeled Property Graph), data organization techniques (e.g., storing graph data in indexing structures or dividing data into records), and different aspects of data distribution and query execution (e.g., support for sharding and Atomicity, Consistency, Isolation, Durability). Fifty-one graph database systems are presented and compared, including Neo4j, OrientDB, and Virtuoso. We outline graph database queries and relationships with associated domains (NoSQL stores, graph streaming, and dynamic graph algorithms). Finally, we outline future research and engineering challenges related to graph databases.

Adaptive query compilation in graph databases

Compiling database queries into compact and efficient machine code has proven to be a great technique to improve query performance and exploit characteristics of modern hardware. Particularly for graph database queries, which often execute the exact instructions for processing, this technique can lead to an improvement. Furthermore, compilation frameworks like LLVM provide powerful optimization techniques and support different backends. However, the time for generating and optimizing machine code becomes an issue for short-running queries or queries which could produce early results quickly. In this work, we present an adaptive approach integrating graph query interpretation and compilation. While query compilation and code generation are running in the background, the query execution starts using the interpreter. When the code generation is finished, the execution switches to the compiled code. Our evaluation of the approach using short-running and complex queries show that autonomously switching execution modes helps to improve the runtime of all types of queries and additionally to hide compilation times and the additional latencies of the underlying storage.

Multiple context-free path querying by matrix multiplication

Many graph analysis problems can be formulated as formal language-constrained path querying problems where the formal languages are used as constraints for navigational path queries. Recently, the context-free language (CFL) reachability formulation has become very popular and can be used in many areas, for example, querying graph databases, Resource Description Framework (RDF) analysis. However, the generative capacity of context-free grammars (CFGs) is too weak to generate some complex queries, for example, from natural languages, and the various extensions of CFGs have been proposed. Multiple context-free grammar (MCFG) is one of such extensions of CFGs. Despite the fact that, to the best of our knowledge, there is no algorithm for MCFL-reachability, this problem is known to be decidable. This paper is devoted to developing the first such algorithm for the MCFL-reachability problem. The essence of the proposed algorithm is to use a set of Boolean matrices and operations on them to find paths in a graph that satisfy the given constraints. The main operation here is Boolean matrix multiplication. As a result, the algorithm returns a set of matrices containing all information needed to solve the MCFL-reachability problem. The presented algorithm is implemented in Python using GraphBLAS API. An analysis of real RDF data and synthetic graphs for some MCFLs is performed. The study showed that using a sparse format for matrix storage and parallel computing for graphs with tens of thousands of edges the analysis time can be 10–20 minutes. The result of the analysis provides tens of millions of reachable vertex pairs. The proposed algorithm can be applied in problems of static code analysis, bioinformatics, network analysis, as well as in graph databases when a path query cannot be expressed using context-free grammars. The provided algorithm is linear algebra-based, hence, it allows one to use high-performance libraries and utilize modern parallel hardware.

Representing Paths in Graph Database Pattern Matching

Modern graph database query languages such as GQL, SQL/PGQ, and their academic predecessor G-Core promote paths to first-class citizens in the sense that their pattern matching facility can return paths , as opposed to only nodes and edges. This is challenging for database engines, since graphs can have a large number of paths between a given node pair, which can cause huge intermediate results in query evaluation. We introduce the concept of path multiset representations (PMRs) , which can represent multisets of paths exponentially succinctly and therefore bring significant advantages for representing intermediate results. We give a detailed theoretical analysis that shows that they are especially well-suited for representing results of regular path queries and extensions thereof involving counting, random sampling, and unions. Our experiments show that they drastically improve scalability for regular path query evaluation, with speedups of several orders of magnitude.

Jumping Evaluation of Nested Regular Path Queries

Nested regular path queries are used for querying graph databases and RDF triple stores. We propose a new algorithm for evaluating nested regular path queries on a graph from a set of start nodes in combined linear time. We show that this complexity upper bound can be reduced by making it dependent on the size of the query's top-down needed subgraph, a notion that we introduce. For many queries in practice, the top-down needed subgraph is way smaller than the whole graph. Our algorithm is based on a novel compilation schema from nested regular path queries to monadic datalog queries. Its complexity upper bound follows from known properties of top-down datalog evaluation. As an application, we show that our algorithm permits to reformulate in simple terms a variant of a very efficient automata-based algorithm proposed by Maneth and Nguyen that evaluates navigational path queries in datatrees based on indexes and jumping. Moreover, it overcomes some limitations of Maneth and Nguyen's: it is not bound to trees and applies to graphs; it is not limited to forward navigational XPath but can treat any nested regular path query and it can be implemented efficiently without any dedicated techniques, by using any efficient datalog evaluator such as LogicBlox.

Modular Path Queries with Arithmetic

We propose a new approach to querying graph databases. Our approach balances competing goals of expressive power, language clarity and computational complexity. A distinctive feature of our approach is the ability to express properties of minimal (e.g. shortest) and maximal (e.g. most valuable) paths satisfying given criteria. To express complex properties in a modular way, we introduce labelling-generating ontologies. The resulting formalism is computationally attractive - queries can be answered in non-deterministic logarithmic space in the size of the database.

Research on Power Equipment System of Knowledge Graph under Electric Energy in Smart Grid

In order to realize technological innovation in the electric power field, the article uses artificial intelligence, big data analysis and mining, knowledge graphs, natural language processing and other technologies to construct Chinese professional dictionaries and knowledge graphs in the electric power field. And on this basis, the thesis puts forward the technical architecture of a comprehensive energy service support system based on the concept of “a picture of the power grid”, a spatiotemporal data management platform and a graph database query application implementation mechanism. Finally, research and design the visualization of the hierarchical organization of the data, use the association relationship between the data to organize the data into multi-topic classification and hierarchical organization, and provide a friendly interactive man-machine interface.

Efficient Authorization of Graph-database Queries in an Attribute-supporting ReBAC Model

Neo4j is a popular graph database that offers two versions: an enterprise edition and a community edition . The enterprise edition offers customizable Role-based Access Control features through custom developed procedures , while the community edition does not offer any access control support. Being a graph database, Neo4j appears to be a natural application for Relationship-Based Access Control (ReBAC), an access control paradigm where authorization decisions are based on relationships between subjects and resources in the system (i.e., an authorization graph). In this article, we present AReBAC, an attribute-supporting ReBAC model for Neo4j that provides finer-grained access control by operating over resources instead of procedures. AReBAC employs Nano-Cypher, a declarative policy language based on Neo4j’s Cypher query language, the result of which allows us to weave database queries with access control policies and evaluate both simultaneously. Evaluating the combined query and policy produces a result that (i) matches the search criteria, and (ii) the requesting subject is authorized to access. AReBAC is accompanied by the algorithms and their implementation required for the realization of the presented ideas, including GP-Eval, a query evaluation algorithm. We also introduce Live-End Backjumping (LBJ), a backtracking scheme that provides a significant performance boost over conflict-directed backjumping for evaluating queries. As demonstrated in our previous work, the original version of GP-Eval already performs significantly faster than the Neo4j’s Cypher evaluation engine. The optimized version of GP-Eval , which employs LBJ, further improves the performance significantly, thereby demonstrating the capabilities of the technique.

Query Acceleration of Graph Databases by ID Caching Technology

In this paper, we approach the design of ID caching technology (IDCT) for graph databases, with the purpose of accelerating the queries on graph database data and avoiding redundant graph database query operations which will consume great computer resources. Traditional graph database caching technology (GDCT) needs a large memory to store data and has the problems of serious data consistency and low cache utilization. To address these issues, in the paper we propose a new technology which focuses on ID allocation mechanism and high-speed queries of ID on graph databases. Specifically, ID of the query result is cached in memory and data consistency is achieved through the real-time synchronization and cache memory adaptation. In addition, we set up complex queries and simple queries to satisfy all query requirements and design a mechanism of cache replacement based on query action time, query times, and memory capacity, thus improving the performance furthermore. Extensive experiments show the superiority of our techniques compared with the traditional query approach of graph databases.

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.

SummaryKnowledge graphs (KGs) are quickly becoming a common-place tool for storing relationships between entities from which higher-level reasoning can be conducted. KGs are typically stored in a graph-database format, and graph-database queries can be used to answer questions of interest that have been posed by users such as biomedical researchers. For simple queries, the inclusion of direct connections in the KG and the storage and analysis of query results are straightforward; however, for complex queries, these capabilities become exponentially more challenging with each increase in complexity of the query. For instance, one relatively complex query can yield a KG with hundreds of thousands of query results. Thus, the ability to efficiently query, store, rank and explore sub-graphs of a complex KG represents a major challenge to any effort designed to exploit the use of KGs for applications in biomedical research and other domains. We present Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways as an abstraction layer and user interface to more easily query KGs and store, rank and explore query results.Availability and implementationAn instance of the ROBOKOP UI for exploration of the ROBOKOP Knowledge Graph can be found at http://robokop.renci.org. The ROBOKOP Knowledge Graph can be accessed at http://robokopkg.renci.org. Code and instructions for building and deploying ROBOKOP are available under the MIT open software license from https://github.com/NCATS-Gamma/robokop.Supplementary information Supplementary data are available at Bioinformatics online.

Automated reasoning for attributed graph properties

Graphs are ubiquitous in computer science. Moreover, in various application fields, graphs are equipped with attributes to express additional information such as names of entities or weights of relationships. Due to the pervasiveness of attributed graphs, it is highly important to have the means to express properties on attributed graphs to strengthen modeling capabilities and to enable analysis. Firstly, we introduce a new logic of attributed graph properties, where the graph part and attribution part are neatly separated. The graph part is equivalent to first-order logic on graphs as introduced by Courcelle. It employs graph morphisms to allow the specification of complex graph patterns. The attribution part is added to this graph part by reverting to the symbolic approach to graph attribution, where attributes are represented symbolically by variables whose possible values are specified by a set of constraints making use of algebraic specifications. Secondly, we extend our refutationally complete tableau-based reasoning method as well as our symbolic model generation approach for graph properties to attributed graph properties. Due to the new logic mentioned above, neatly separating the graph and attribution parts, and the categorical constructions employed only on a more abstract level, we can leave the graph part of the algorithms seemingly unchanged. For the integration of the attribution part into the algorithms, we use an oracle, allowing for flexible adoption of different available SMT solvers in the actual implementation. Finally, our automated reasoning approach for attributed graph properties is implemented in the tool AutoGraph integrating in particular the SMT solver Z3 for the attribute part of the properties. We motivate and illustrate our work with a particular application scenario on graph database query validation.

Functional querying in graph databases

The paper is focused on a functional querying in graph databases. We consider labelled property graph model and mention also the graph model behind XML databases. An attention is devoted to functional modelling of graph databases both at a conceptual and data level. The notions of graph conceptual schema and graph database schema are considered. The notion of a typed attribute is used as a basic structure both on the conceptual and database level. As a formal approach to declarative graph database querying a version of typed lambda calculus is used. This approach allows to use a logic necessary for querying, arithmetic as well as aggregation function. Another advantage is the ability to deal with relations and graphs in one integrated environment.

High-Performance with an In-GPU Graph Database Cache

Although graph databases have great potential to directly represent huge and complex network structures, such as social and logistics networks, they currently do not perform well enough. To achieve a two-orders-of-magnitude performance improvement on graph database queries, the authors propose caching the graph database in distributed GPUs connected with a 10-Gbit Ethernet (10GbE) network. Property read, traverse, and graph search queries are accelerated by 25.9, 252.4, and 383.2 times, respectively, compared to those using Neo4j for a huge graph consisting of 3.2 million nodes whose degree is 100.

The algebra of recursive graph transformation language UnCAL: complete axiomatisation and iteration categorical semantics

The aim of this paper is to provide mathematical foundations of a graph transformation language, called UnCAL, using categorical semantics of type theory and fixed points. About 20 years ago, Bunemanet al. developed a graph database query language UnQL on the top of a functional meta-language UnCAL for describing and manipulating graphs. Recently, the functional programming community has shown renewed interest in UnCAL, because it provides an efficient graph transformation language which is useful for various applications, such as bidirectional computation.In order to make UnCAL more flexible and fruitful for further extensions and applications, in this paper, we give a more conceptual understanding of UnCAL using categorical semantics. Our general interest of this paper is to clarify what is the algebra of UnCAL. Thus, we give an equational axiomatisation and categorical semantics of UnCAL, both of which are new. We show that the axiomatisation is complete for the original bisimulation semantics of UnCAL. Moreover, we provide a clean characterisation of the computation mechanism of UnCAL called ‘structural recursion on graphs’ using our categorical semantics. We show a concrete model of UnCAL given by the λG-calculus, which shows an interesting connection to lazy functional programming.

Iteration Algebras for UnQL Graphs and Completeness for Bisimulation

This paper shows an application of Bloom and Esik's iteration algebras to model graph data in a graph database query language. About twenty years ago, Buneman et al. developed a graph database query language UnQL on the top of a functional meta-language UnCAL for describing and manipulating graphs. Recently, the functional programming community has shown renewed interest in UnCAL, because it provides an efficient graph transformation language which is useful for various applications, such as bidirectional computation. However, no mathematical semantics of UnQL/UnCAL graphs has been developed. In this paper, we give an equational axiomatisation and algebraic semantics of UnCAL graphs. The main result of this paper is to prove that completeness of our equational axioms for UnCAL for the original bisimulation of UnCAL graphs via iteration algebras. Another benefit of algebraic semantics is a clean characterisation of structural recursion on graphs using free iteration algebra.

XPath for DL Ontologies

Applications of description logics (DLs) such as ontology-based data access (OBDA) require understanding of how to pose database queries over DL knowledge bases. While there have been many studies regarding traditional relational query formalisms such as conjunctive queries and their extensions, little attention has been paid to graph database queries, despite the fact that graph databases have essentially the same structure as knowledge bases. In particular, not much is known about the interplay between DLs and XPath. The latter is a powerful formalism for querying semistructured data: it is in the core of most practical query languages for XML trees, and it is also gaining popularity in theory and practice of graph databases. In this paper we make a step towards coupling knowledge bases and graph databases by studying how to answer powerful XPath-style queries over simple DLs like DL-Lite and EL. We start with adapting the definition of XPath to the DL context, and then proceed to study the complexity of evaluating XPath queries over knowledge bases. Results show that, while query answering is undecidable for the full XPath, by carefully tuning the shape of negation allowed in the queries we can arrive at XPath fragments that have a potential to be used in practice.

Are graph databases ready for bioinformatics?

Contact: Lars.Juhl.Jensen@gmail.com

Parameterized regular expressions and their languages

We study regular expressions that use variables, or parameters, which are interpreted as alphabet letters. We consider two classes of languages denoted by such expressions: under the possibility semantics, a word belongs to the language if it is denoted by some regular expression obtained by replacing variables with letters; under the certainty semantics, the word must be denoted by every such expression. Such languages are regular, and we show that they naturally arise in several applications such as querying graph databases and program analysis. As the main contribution of the paper, we provide a complete characterization of the complexity of the main computational problems related to such languages: nonemptiness, universality, containment, membership, as well as the problem of constructing NFAs capturing such languages. We also look at the extension when domains of variables could be arbitrary regular languages, and show that under the certainty semantics, languages remain regular and the complexity of the main computational problems does not change.