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Property graphs are popular in both industry and academia due to their versatility in modeling complex data across diverse application domains, ranging from social networks to knowledge graphs. Despite their popularity, there is no standardized data format for storing and exchanging property graphs. This paper introduces PGDF, a text-based data format for property graphs, designed to be both simple and flexible, while remaining expressive and efficient. The simplicity of PGDF comes from its tabular-like structure, where each line in a PGDF file contains a single schema or data declaration. PGDF offers great flexibility by allowing schema and data declarations to be combined in any order. This means that nodes and edges can each have their own distinct properties, providing greater adaptability and customization. The expressiveness of PGDF is defined by its ability to represent a wide range of property graph features. In this article, we describe the syntax and semantics of PGDF, outline methods for converting property graphs stored in multiple CSV files to PGDF and other graph data formats, and present an experimental evaluation comparing PGDF, YARS-PG, GraphML, and JSON-Neo4j. The experiments show that PGDF enables the production of smaller files more quickly compared to other graph data formats.

Conceptual schemas are the basis to build well-grounded Information Systems, by representing the main concepts of a domain of knowledge, as well as the relationships among them. Since conceptual schemas focus on the concepts, they are independent of the specific technological platform used to implement them. This allows a single conceptual schema to be transformed into different platform-specific models according to the implementation requirements. This is a non-trivial process that is crucial for the performance and maintainability of the system, as well as for the accomplishment of the domain data requirements. Much research has been done on transforming conceptual schemas into relational data models. Nevertheless, less work has been done on transforming conceptual schemas into property graphs, a data structure indispensable to building appropriate and efficient systems based on graph databases. The work proposes a systematic approach to transform conceptual schemas, represented as UML class diagrams, into property graphs by using a set of transformation rules and patterns applied in a systematic way. Besides a practical example used to help the presentation of the proposed approach, the evaluation has been done by measuring different quality dimensions such as semantic equivalence, readability, maintainability, complexity, size, and performance. [ABSTRACT FROM AUTHOR]

Temporal graphs represent graph evolution over time, and have been receiving considerable research attention. Work on expressing temporal graph patterns or discovering temporal motifs typically assumes relatively simple temporal constraints, such as journeys or, more generally, existential constraints, possibly with finite delays. In this paper we propose to use timed automata to express temporal constraints, leading to a general and powerful notion of temporal basic graph pattern (BGP). The new difficulty is the evaluation of the temporal constraint on a large set of matchings. An important benefit of timed automata is that they support an iterative state assignment, which can be useful for early detection of matches and pruning of non-matches. We introduce algorithms to retrieve all instances of a temporal BGP match in a graph, and present results of an extensive experimental evaluation, demonstrating interesting performance trade-offs. We show that an on-demand algorithm that processes total matchings incrementally over time is preferable when dealing with cyclic patterns on sparse graphs. On acyclic patterns or dense graphs, and when connectivity of partial matchings can be guaranteed, the best performance is achieved by maintaining partial matchings over time and allowing automaton evaluation to be fully incremental. The code and datasets used in our analysis are available at http://github.com/amirpouya/TABGP. [ABSTRACT FROM AUTHOR]

Abstract Protecting medical privacy can create obstacles in the analysis and distribution of healthcare graphs and statistical inferences accompanying them. We pose a graph simulation model which generates networks using degree and property augmentation and provide a flexible R package that allows users to create graphs that preserve vertex attribute relationships and approximating the retention of topological properties observed in the original graph (e.g., community structure). We illustrate our proposed algorithm using a case study based on Zachary’s karate network and a patient-sharing graph generated from Medicare claims data in 2019. In both cases, we find that community structure is preserved, and normalized root mean square error between cumulative distributions of the degrees across the generated and the original graphs is low (0.0508 and 0.0514 respectively).

Nowadays there is a great interest in the visualization of property graphs to make their navigation, inspection, and visual analysis easier. However, property graphs can be quite large and their rendering on web browsers can lead to a dark cloud of points that is difficult to visually explore. With the aim of reducing the size of the visualized graph, several approaches have been proposed for substituting clusters of related vertices with aggregated meta-nodes and introducing meta-edges among them, but they usually consider the graph in main-memory and do not adopt efficient data structures for extracting parts of it from the disk. The purpose of this paper is to optimize the preparation of the graph to be visualized according to a certain resolution level by introducing refined data structures and specifically tailored algorithms. By means of them, the rendering time is reduced when changing the current visualization through zoom-in, zoom-out, and related operations. Starting from a cluster hierarchy that represents the possible aggregations of graph nodes, in the paper we characterize a visualization according to a horizontal slice of the hierarchy and propose indexing structures and incremental algorithms for quickly passing to a new visualization with minimal changes of the current one. In this process, we ensure a consistent and efficient aggregation of addictive properties associated with nodes and edges. An extensive experimental analysis has been conducted to assess the quality of the proposed solution.

Within the PREDIMED Clinical Data Warehouse (CDW) of Grenoble Alpes University Hospital (CHUGA), we have developed a hypergraph based operational data model, aiming at empowering physicians to explore, visualize and qualitatively analyze interactively the complex and massive information of the patients treated in CHUGA. This model constitutes a central target structure, expressed in a dual form, both graphical and formal, which gathers the concepts and their semantic relations into a hypergraph whose implementation can easily be manipulated by medical experts. The implementation is based on a property graph database linked to an interactive graphical interface allowing to navigate through the data and to interact in real time with a search engine, visualization and analysis tools. This model and its agile implementation allow for easy structural changes inherent to the evolution of techniques and practices in the health field. This flexibility provides adaptability to the evolution of interoperability standards. [ABSTRACT FROM AUTHOR]

RDF and Property Graphs are data models that are being used to represent Knowledge Graphs. The definition of methods to transform RDF data into Property graph data is fundamental to allow interoperability among the systems using these models. Although both models are based on a graph structure, they have special features that complicate the definition of data transformation methods. This article presents an ontology-based approach to transform (automatically) property graphs into RDF graphs. The ontology, called PGO, defines a set of terms that allows describing the elements of a property graph. The algorithm corresponding to the transformation method is described, and some properties of the method are discussed (complexity, data preservation, and monotonicity). The results of an experimental evaluation are also presented.

In this paper, we propose a compact data structure to store labeled attributed graphs based on the k 2 -tree, which is a very compact data structure designed to represent a simple directed graph. The idea we propose can be seen as an extension of the k 2 -tree to support property graphs. In addition to the static approach, we also propose a dynamic version of the storage representation, which allows flexible schemas and insertion or deletion of data. We provide an implementation of a basic set of operations, which can be combined to form complex queries over these graphs with attributes. We evaluate the performance of our proposal with existing graph database systems and prove that our compact attributed graph representation obtains also competitive time results. [ABSTRACT FROM AUTHOR]

We survey foundational features underlying modern graph query languages. We first discuss two popular graph data models: edge-labelled graphs, where nodes are connected by directed, labelled edges and property graphs, where nodes and edges can further have attributes. Next we discuss the two most fundamental graph querying functionalities: graph patterns and navigational expressions. We start with graph patterns, in which a graph-structured query is matched against the data. Thereafter, we discuss navigational expressions, in which patterns can be matched recursively against the graph to navigate paths of arbitrary length; we give an overview of what kinds of expressions have been proposed and how they can be combined with graph patterns.We also discuss several semantics under which queries using the previous features can be evaluated, what effects the selection of features and semantics has on complexity, and offer examples of such features in three modern languages that are used to query graphs: SPARQL, Cypher and Gremlin. We conclude by discussing the importance of formalisation for graph query languages; a summary of what is known about SPARQL, Cypher and Gremlin in terms of expressivity and complexity; and an outline of possible future directions for the area. [ABSTRACT FROM AUTHOR]

• A method of exploring RDF triples is proposed for user to manipulate property graphs interactively. • To improve exploration efficiency, RDF triples are persisted in graph databases. • We implement an RDF exploration system PG-Explorer and its usability is evaluated. The Resource Description Framework (RDF) has been widely applied to represent and exchange domain information because of its machine-readable characteristic. With a huge amount of RDF data available, retrieving RDF data is essential, so that many RDF query approaches have been developed. But many traditional approaches generally require users to know RDF model and query language, and this seriously prevents a large number of common non-expert users from obtaining information in RDF datasets. In this paper, we propose an approach that users can explore massive RDF datasets by interactively manipulating property graphs. Our approach provides users with a series of operations in interactively constructing property graphs to describe their query intents. To efficiently explore massive RDF datasets, we convert RDF data into property graphs for storage. This can greatly reduce the size of massive RDF datasets and more importantly the converted property graphs can instruct users to understand the underlying structure of RDF datasets, which is very useful in users' construction of their query property graphs. The constructed query property graphs are finally transformed into expressions with the query language of graph databases. With high-performance graph databases as query engines, we developed an RDF data exploration system – PG-Explorer. Through experiments over real-world datasets, we evaluated the effectiveness and superiority of our approach. The user study demonstrates that the proposed approach simplifies users' exploration of RDF data and can satisfy their exploration needs. [ABSTRACT FROM AUTHOR]

Multiscale models are commonplace in cancer modeling, where individual models acting on different biological scales are combined within a single, cohesive modeling framework. However, model composition gives rise to challenges in understanding interfaces and interactions between them. Based on specific domain expertise, typically these computational models are developed by separate research groups using different methodologies, programming languages, and parameters. This paper introduces a graph-based model for semantically linking computational cancer models via domain graphs that can help us better understand and explore combinations of models spanning multiple biological scales. We take the data model encoded by TumorML, an XML-based markup language for storing cancer models in online repositories, and transpose its model description elements into a graph-based representation. By taking such an approach, we can link domain models, such as controlled vocabularies, taxonomic schemes, and ontologies, with cancer model descriptions to better understand and explore relationships between models. The union of these graphs creates a connected property graph that links cancer models by categorizations, by computational compatibility, and by semantic interoperability, yielding a framework in which opportunities for exploration and discovery of combinations of models become possible.