An introduction to Graph Data Management

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 graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

PathSys: integrating molecular interaction graphs for systems biology

BACKGROUND: The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. RESULTS: Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. CONCLUSION: Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at

Autonomic disaggregated multilayer networking

Focused on reducing capital expenditures by opening the data plane to multiple vendors without impacting performance, node disaggregation is attracting the interest of network operators. Although the software-defined networking (SDN) paradigm is key for the control of such networks, the increased complexity of multilayer networks strictly requires monitoring/telemetry and data analytics capabilities to assist in creating and operating self-managed (autonomic) networks. Such autonomicity greatly reduces operational expenditures, while improving network performance. In this context, a monitoring and data analytics (MDA) architecture consisting of centralized data storage with data analytics capabilities, together with a generic node agent for monitoring/telemetry supporting disaggregation, is presented. A YANG data model that allows one to clearly separate responsibilities for monitoring configuration from node configuration is also proposed. The MDA architecture and YANG data models are experimentally demonstrated through three different use cases: i) virtual link creation supported by an optical connection, where monitoring is automatically activated; ii) multilayer self-configuration after bit error rate (BER) degradation detection, where a modulation format adaptation is recommended for the SDN controller to minimize errors (this entails reducing the capacity of both the virtual link and supported multiprotocol label switching-transport profile (MPLS-TP) paths); and iii) optical layer selfhealing, including failure localization at the optical layer to find the cause of BER degradation. A combination of active and passive monitoring procedures allows one to localize the cause of the failure, leading to lightpath rerouting recommendations toward the SDN controller avoiding the failing element(s).Peer ReviewedPostprint (author's final draft

Comparative analysis of PropertyFirst vs. EntityFirst modeling approaches in graph databases

While relational databases still hold the primary position in the database technology domain, and have been for the longest time of any Computer Science technology has since its inception, for the first time the relational databases now have valid and worthy opponent in the NoSQL database movement. NoSQL databases, even though not many people have heard of them, with a significant number of Computer Science people included, have spread rapidly in many shapes and forms and have done so in quite a chaotic fashion. Similarly to the way they appeared and spread, design and modeling for them have been undertaken in an unstructured manner. Currently they are subcategorized in 4 main groups as: Key-value stores, Column Family stores, Document stores and Graph databases. In this thesis, different modeling approaches for graph databases, applied to the same domain are analyzed and compared, especially from a design perspective. The database selected here as the implemented technology is Neo4J by Neo Technologies and is a directed property graph database, which means that relationships between its data entities must have a starting and ending (or source and destination) node. This research provides an overview of two competing modeling approaches and evaluates them in a context of a real world example. The work done here shows that both of these modeling approaches are valid and that it is possible to fully develop a data model based on the same domain data with both approaches and that both can be used later to support application access in a similar fashion. One of the models provides for faster access to data, but at a cost of higher maintenance and increased complexity

Quarry: A user-centered big data integration platform

Obtaining valuable insights and actionable knowledge from data requires cross-analysis of domain data typically coming from various sources. Doing so, inevitably imposes burdensome processes of unifying different data formats, discovering integration paths, and all this given specific analytical needs of a data analyst. Along with large volumes of data, the variety of formats, data models, and semantics drastically contribute to the complexity of such processes. Although there have been many attempts to automate various processes along the Big Data pipeline, no unified platforms accessible by users without technical skills (like statisticians or business analysts) have been proposed. In this paper, we present a Big Data integration platform (Quarry) that uses hypergraph-based metadata to facilitate (and largely automate) the integration of domain data coming from a variety of sources, and provides an intuitive interface to assist end users both in: (1) data exploration with the goal of discovering potentially relevant analysis facets, and (2) consolidation and deployment of data flows which integrate the data, and prepare them for further analysis (descriptive or predictive), visualization, and/or publishing. We validate Quarry’s functionalities with the use case of World Health Organization (WHO) epidemiologists and data analysts in their fight against Neglected Tropical Diseases (NTDs).This work is partially supported by GENESIS project, funded by the Spanish Ministerio de Ciencia, Innovación y Universidades under project TIN2016-79269-R.Peer ReviewedPostprint (author's final draft

MDG-NoSQL : modelo de dados para bancos NoSQL baseados em grafos

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2015.Os bancos de dados em grafo vêm se tornando populares juntamente com as demais iniciativas NoSQL. Porém, os bancos de dados em grafos não possuem uma notação padrão. Sendo assim, o presente trabalho agrupa diversas notações e propostas de modelagem em grafos, construindo um novo modelo, chamado de Modelo de Dados para Bancos NoSQL Baseados em Grafos (MDG-NoSQL), com recursos para agrupar em uma notação as características dos bancos de dados em grafos. Esse modelo foi validado utilizando a implementação de um banco de dados de vínculos societários de empresas, combinados com os relacionamentos dessas pessoas jurídicas com os processos de compras, também chamadas de licitações, junto ao Governo Federal (Banco de Vínculos Simpli_cado para Licitações e Sociedades). Esse estudo de caso foi direcionado para auxiliar na detecção de fraudes em processos licitatórios que, além de ser diretamente aplicável a vários órgãos de controle, perícia e inteligência em âmbito nacional, permite extrair fundamentos extens íveis a outros problemas com modelagens de vínculos.Currently, Graph Databases are becoming popular along with other NoSQL initiatives. Thus, researchers and companies have been developing data models to manipulate information as graphs However, there is no standard notation involves several features and structures of the graph databases. This model introduces several notations and concepts for building a new graph data model, called Data Model for NoSQL Graph Databases (GDM-NoSQL). The GDM-NoSQL was veri_ed through a database for investigate relationships between companies and people as well as information about the procurements that these companies participated in with the Federal Government. This database was designed to facilitate the process of searching for frauds and to be used on multiple contexts, i.e. several di_erent national agencies. Finally, the designed model was implemented in both a relational and a graph database in order to validate the hypothesis that writing relationships is simpler and more e_cient in graph models than relational databases

Architectural explorations for streaming accelerators with customized memory layouts

El concepto básico de la arquitectura mono-nucleo en los procesadores de propósito general se ajusta bien a un modelo de programación secuencial. La integración de multiples núcleos en un solo chip ha permitido a los procesadores correr partes del programa en paralelo. Sin embargo, la explotación del enorme paralelismo disponible en muchas aplicaciones de alto rendimiento y de los datos correspondientes es difícil de conseguir usando unicamente multicores de propósito general. La aparición de aceleradores tipo streaming y de los correspondientes modelos de programación han mejorado esta situación proporcionando arquitecturas orientadas al proceso de flujos de datos. La idea básica detrás del diseño de estas arquitecturas responde a la necesidad de procesar conjuntos enormes de datos. Estos dispositivos de alto rendimiento orientados a flujos permiten el procesamiento rapido de datos mediante el uso eficiente de computación paralela y comunicación entre procesos. Los aceleradores streaming orientados a flujos, igual que en otros procesadores, consisten en diversos componentes micro-arquitectonicos como por ejemplo las estructuras de memoria, las unidades de computo, las unidades de control, los canales de Entrada/Salida y controles de Entrada/Salida, etc. Sin embargo, los requisitos del flujo de datos agregan algunas características especiales e imponen otras restricciones que afectan al rendimiento. Estos dispositivos, por lo general, ofrecen un gran número de recursos computacionales, pero obligan a reorganizar los conjuntos de datos en paralelo, maximizando la independiencia para alimentar los recursos de computación en forma de flujos. La disposición de datos en conjuntos independientes de flujos paralelos no es una tarea sencilla. Es posible que se tenga que cambiar la estructura de un algoritmo en su conjunto o, incluso, puede requerir la reescritura del algoritmo desde cero. Sin embargo, todos estos esfuerzos para la reordenación de los patrones de las aplicaciones de acceso a datos puede que no sean muy útiles para lograr un rendimiento óptimo. Esto es debido a las posibles limitaciones microarquitectonicas de la plataforma de destino para los mecanismos hardware de prefetch, el tamaño y la granularidad del almacenamiento local, y la flexibilidad para disponer de forma serial los datos en el interior del almacenamiento local. Las limitaciones de una plataforma de streaming de proposito general para el prefetching de datos, almacenamiento y demas procedimientos para organizar y mantener los datos en forma de flujos paralelos e independientes podría ser eliminado empleando técnicas a nivel micro-arquitectonico. Esto incluye el uso de memorias personalizadas especificamente para las aplicaciones en el front-end de una arquitectura streaming. El objetivo de esta tesis es presentar exploraciones arquitectónicas de los aceleradores streaming con diseños de memoria personalizados. En general, la tesis cubre tres aspectos principales de tales aceleradores. Estos aspectos se pueden clasificar como: i) Diseño de aceleradores de aplicaciones específicas con diseños de memoria personalizados, ii) diseño de aceleradores con memorias personalizadas basados en plantillas, y iii) exploraciones del espacio de diseño para dispositivos orientados a flujos con las memorias estándar y personalizadas. Esta tesis concluye con la propuesta conceptual de una Blacksmith Streaming Architecture (BSArc). El modelo de computación Blacksmith permite la adopción a nivel de hardware de un front-end de aplicación específico utilizando una GPU como back-end. Esto permite maximizar la explotación de la localidad de datos y el paralelismo a nivel de datos de una aplicación mientras que proporciona un flujo mayor de datos al back-end. Consideramos que el diseño de estos procesadores con memorias especializadas debe ser proporcionado por expertos del dominio de aplicación en la forma de plantillas.The basic concept behind the architecture of a general purpose CPU core conforms well to a serial programming model. The integration of more cores on a single chip helped CPUs in running parts of a program in parallel. However, the utilization of huge parallelism available from many high performance applications and the corresponding data is hard to achieve from these general purpose multi-cores. Streaming accelerators and the corresponding programing models improve upon this situation by providing throughput oriented architectures. The basic idea behind the design of these architectures matches the everyday increasing requirements of processing huge data sets. These high-performance throughput oriented devices help in high performance processing of data by using efficient parallel computations and streaming based communications. The throughput oriented streaming accelerators ¿ similar to the other processors ¿ consist of numerous types of micro-architectural components including the memory structures, compute units, control units, I/O channels and I/O controls etc. However, the throughput requirements add some special features and impose other restrictions for the performance purposes. These devices, normally, offer a large number of compute resources but restrict the applications to arrange parallel and maximally independent data sets to feed the compute resources in the form of streams. The arrangement of data into independent sets of parallel streams is not an easy and simple task. It may need to change the structure of an algorithm as a whole or even it can require to write a new algorithm from scratch for the target application. However, all these efforts for the re-arrangement of application data access patterns may still not be very helpful to achieve the optimal performance. This is because of the possible micro-architectural constraints of the target platform for the hardware pre-fetching mechanisms, the size and the granularity of the local storage and the flexibility in data marshaling inside the local storage. The constraints of a general purpose streaming platform on the data pre-fetching, storing and maneuvering to arrange and maintain it in the form of parallel and independent streams could be removed by employing micro-architectural level design approaches. This includes the usage of application specific customized memories in the front-end of a streaming architecture. The focus of this thesis is to present architectural explorations for the streaming accelerators using customized memory layouts. In general the thesis covers three main aspects of such streaming accelerators in this research. These aspects can be categorized as : i) Design of Application Specific Accelerators with Customized Memory Layout ii) Template Based Design Support for Customized Memory Accelerators and iii) Design Space Explorations for Throughput Oriented Devices with Standard and Customized Memories. This thesis concludes with a conceptual proposal on a Blacksmith Streaming Architecture (BSArc). The Blacksmith Computing allow the hardware-level adoption of an application specific front-end with a GPU like streaming back-end. This gives an opportunity to exploit maximum possible data locality and the data level parallelism from an application while providing a throughput natured powerful back-end. We consider that the design of these specialized memory layouts for the front-end of the device are provided by the application domain experts in the form of templates. These templates are adjustable according to a device and the problem size at the device's configuration time. The physical availability of such an architecture may still take time. However, simulation framework helps in architectural explorations to give insight into the proposal and predicts potential performance benefits for such an architecture

Κατανεμημένη αποτίμηση επερωτήσεων και συλλογιστική για το μοντέλο RDF σε δίκτυα ομοτίμων κόμβων

Με το ενδιαφέρον για τις εφαρμογές του Σημασιολογικού Ιστού να αυξάνεται ραγδαία, το μοντέλο RDF και RDFS έχει γίνει ένα από τα πιο ευρέως χρησιμοποιούμενα μοντέλα δεδομένων για την αναπαράσταση και την ενσωμάτωση δομημένης πληροφορίας στον Ιστό. Το πλήθος των διαθέσιμων πηγών πληροφορίας RDF συνεχώς αυξάνεται με αποτέλεσμα να υπάρχει μια επιτακτική ανάγκη για τη διαχείριση RDF δεδομένων. Σε αυτή τη διατριβή επικεντρωνόμαστε στην κατανεμημένη διαχείριση RDF δεδομένων σε δίκτυα ομότιμων κόμβων. Σχεδιάζουμε και υλοποιούμε το σύστημα Atlas, ένα πλήρως κατανεμημένο σύστημα για την αποθήκευση RDF και RDFS δεδομένων, την αποτίμηση και βελτιστοποίηση επερωτήσεων στη γλώσσα SPARQL και τη συλλογιστική στο μοντέλο RDFS. Το σύστημα Atlas χρησιμοποιεί κατανεμημένους πίνακες κατακερματισμού, μια δημοφιλή περίπτωση δικτύων ομότιμων κόμβων. Αρχικά, αναλύουμε κατανεμημένους αλγόριθμους για συλλογιστική RDFS χρησιμοποιώντας κατανεμημένους πίνακες κατακερματισμού. Υλοποιηούμε διάφορες παραλλαγές των αλγορίθμων προς τα εμπρός αλυσίδα εκτέλεσης και προς τα πίσω αλυσίδα εκτέλεσης καθώς και έναν αλγόριθμο που χρησιμοποιεί την τεχνική μετασχηματισμού των κανόνων σε μαγικό σύνολο. Αποδεικνύουμε θεωρητικά την ορθότητα των αλγορίθμων αυτών και προσφέρουμε μια συγκριτική μελέτη τόσο αναλυτικά όσο και πειραματικά. Παράλληλα, προτείνουμε αλγορίθμους και τεχνικές για την αποτίμηση και τη βελτιστοποίηση επερωτήσεων στη γλώσσα SPARQL για RDF δεδομένα που είναι αποθηκευμένα σε κατανεμημένους πίνακες κατακερματισμού. Οι τεχνικές βελτιστοποίησης βασίζονται σε εκτιμήσεις επιλεκτικότητας και έχουν στόχο τη μείωση του χρόνου απόκρισης της επερώτησης καθώς και της κατανάλωσης εύρους ζώνης του δικτύου. Η εκτεταμένη πειραματική αξιολόγηση των μεθόδων βελτιστοποίησης γίνεται σε μια τοπική συστάδα υπολογιστών χρησιμοποιώντας ένα ευρέως διαδεδομένο σημείο αναφοράς μετρήσεων.With the interest in Semantic Web applications rising rapidly, the Resource Description Framework (RDF) and its accompanying vocabulary description language, RDF Schema (RDFS), have become one of the most widely used data models for representing and integrating structured information in the Web. With the vast amount of available RDF data sources on the Web increasing rapidly, there is an urgent need for RDF data management. In this thesis, we focus on distributed RDF data management in peer-to-peer (P2P) networks. More specifically, we present results that advance the state-of-the-art in the research area of distributed RDF query processing and reasoning in P2P networks. We fully design and implement a P2P system, called Atlas, for the distributed query processing and reasoning of RDF and RDFS data. Atlas is built on top of distributed hash tables (DHTs), a commonly-used case of P2P networks. Initially, we study RDFS reasoning algorithms on top of DHTs. We design and develop distributed forward and backward chaining algorithms, as well as an algorithm which works in a bottom-up fashion using the magic sets transformation technique. We study theoretically the correctness of our reasoning algorithms and prove that they are sound and complete. We also provide a comparative study of our algorithms both analytically and experimentally. In the experimental part of our study, we obtain measurements in the realistic large-scale distributed environment of PlanetLab as well as in the more controlled environment of a local cluster. Moreover, we propose algorithms for SPARQL query processing and optimization over RDF(S) databases stored on top of distributed hash tables. We fully implement and evaluate a DHT-based optimizer. The goal of the optimizer is to minimize the time for answering a query as well as the bandwidth consumed during the query evaluation. The optimization algorithms use selectivity estimates to determine the chosen query plan. Our algorithms and techniques have been extensively evaluated in a local cluster

Visões em bancos de dados de grafos : uma abordagem multifoco para dados heterogêneos

Orientador: Claudia Maria Bauzer MedeirosTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: A pesquisa científica tornou-se cada vez mais dependente de dados. Esse novo paradigma de pesquisa demanda técnicas e tecnologias computacionais sofisticadas para apoiar tanto o ciclo de vida dos dados científicos como a colaboração entre cientistas de diferentes áreas. Uma demanda recorrente em equipes multidisciplinares é a construção de múltiplas perspectivas sobre um mesmo conjunto de dados. Soluções atuais cobrem vários aspectos, desde o projeto de padrões de interoperabilidade ao uso de sistemas de gerenciamento de bancos de dados não-relacionais. Entretanto, nenhum desses esforços atende de forma adequada a necessidade de múltiplas perspectivas, denominadas focos nesta tese. Em termos gerais, um foco é projetado e construído para atender um determinado grupo de pesquisa (mesmo no escopo de um único projeto) que necessita manipular um subconjunto de dados de interesse em múltiplos níveis de agregação/generalização. A definição e criação de um foco são tarefas complexas que demandam mecanismos capazes de manipular múltiplas representações de um mesmo fenômeno do mundo real. O objetivo desta tese é prover múltiplos focos sobre dados heterogêneos. Para atingir esse objetivo, esta pesquisa se concentrou em quatro principais problemas. Os problemas inicialmente abordados foram: (1) escolher um paradigma de gerenciamento de dados adequado e (2) elencar os principais requisitos de pesquisas multifoco. Nossos resultados nos direcionaram para a adoção de bancos de dados de grafos como solução para o problema (1) e a utilização do conceito de visões, de bancos de dados relacionais, para o problema (2). Entretanto, não há consenso sobre um modelo de dados para bancos de dados de grafos e o conceito de visões é pouco explorado nesse contexto. Com isso, os demais problemas tratados por esta pesquisa são: (3) a especificação de um modelo de dados de grafos e (4) a definição de um framework para manipular visões em bancos de dados de grafos. Nossa pesquisa nesses quatro problemas resultaram nas contribuições principais desta tese: (i) apontar o uso de bancos de dados de grafos como camada de persistência em pesquisas multifoco - um tipo de banco de dados de esquema flexível e orientado a relacionamentos que provê uma ampla compreensão sobre as relações entre os dados; (ii) definir visões para bancos de dados de grafos como mecanismo para manipular múltiplos focos, considerando operações de manipulação de dados em grafos, travessias e algoritmos de grafos; (iii) propor um modelo de dados para grafos - baseado em grafos de propriedade - para lidar com a ausência de um modelo de dados pleno para grafos; (iv) especificar e implementar um framework, denominado Graph-Kaleidoscope, para prover o uso de visões em bancos de dados de grafos e (v) validar nosso framework com dados reais em aplicações distintas - em biodiversidade e em recursos naturais - dois típicos exemplos de pesquisas multidisciplinares que envolvem a análise de interações de fenômenos a partir de dados heterogêneosAbstract: Scientific research has become data-intensive and data-dependent. This new research paradigm requires sophisticated computer science techniques and technologies to support the life cycle of scientific data and collaboration among scientists from distinct areas. A major requirement is that researchers working in data-intensive interdisciplinary teams demand construction of multiple perspectives of the world, built over the same datasets. Present solutions cover a wide range of aspects, from the design of interoperability standards to the use of non-relational database management systems. None of these efforts, however, adequately meet the needs of multiple perspectives, which are called foci in the thesis. Basically, a focus is designed/built to cater to a research group (even within a single project) that needs to deal with a subset of data of interest, under multiple ggregation/generalization levels. The definition and creation of a focus are complex tasks that require mechanisms and engines to manipulate multiple representations of the same real world phenomenon. This PhD research aims to provide multiple foci over heterogeneous data. To meet this challenge, we deal with four research problems. The first two were (1) choosing an appropriate data management paradigm; and (2) eliciting multifocus requirements. Our work towards solving these problems made as choose graph databases to answer (1) and the concept of views in relational databases for (2). However, there is no consensual data model for graph databases and views are seldom discussed in this context. Thus, research problems (3) and (4) are: (3) specifying an adequate graph data model and (4) defining a framework to handle views on graph databases. Our research in these problems results in the main contributions of this thesis: (i) to present the case for the use of graph databases in multifocus research as persistence layer - a schemaless and relationship driven type of database that provides a full understanding of data connections; (ii) to define views for graph databases to support the need for multiple foci, considering graph data manipulation, graph algorithms and traversal tasks; (iii) to propose a property graph data model (PGDM) to fill the gap of absence of a full-fledged data model for graphs; (iv) to specify and implement a framework, named Graph-Kaleidoscope, that supports views over graph databases and (v) to validate our framework for real world applications in two domains - biodiversity and environmental resources - typical examples of multidisciplinary research that involve the analysis of interactions of phenomena using heterogeneous dataDoutoradoCiência da ComputaçãoDoutora em Ciência da Computaçã