On-Demand Big Data Integration: A Hybrid ETL Approach for Reproducible Scientific Research

Scientific research requires access, analysis, and sharing of data that is distributed across various heterogeneous data sources at the scale of the Internet. An eager ETL process constructs an integrated data repository as its first step, integrating and loading data in its entirety from the data sources. The bootstrapping of this process is not efficient for scientific research that requires access to data from very large and typically numerous distributed data sources. a lazy ETL process loads only the metadata, but still eagerly. Lazy ETL is faster in bootstrapping. However, queries on the integrated data repository of eager ETL perform faster, due to the availability of the entire data beforehand. In this paper, we propose a novel ETL approach for scientific data integration, as a hybrid of eager and lazy ETL approaches, and applied both to data as well as metadata. This way, Hybrid ETL supports incremental integration and loading of metadata and data from the data sources. We incorporate a human-in-the-loop approach, to enhance the hybrid ETL, with selective data integration driven by the user queries and sharing of integrated data between users. We implement our hybrid ETL approach in a prototype platform, Obidos, and evaluate it in the context of data sharing for medical research. Obidos outperforms both the eager ETL and lazy ETL approaches, for scientific research data integration and sharing, through its selective loading of data and metadata, while storing the integrated data in a scalable integrated data repository.Comment: Pre-print Submitted to the DMAH Special Issue of the Springer DAPD Journa

Impliance: A Next Generation Information Management Appliance

ably successful in building a large market and adapting to the changes of the last three decades, its impact on the broader market of information management is surprisingly limited. If we were to design an information management system from scratch, based upon today's requirements and hardware capabilities, would it look anything like today's database systems?" In this paper, we introduce Impliance, a next-generation information management system consisting of hardware and software components integrated to form an easy-to-administer appliance that can store, retrieve, and analyze all types of structured, semi-structured, and unstructured information. We first summarize the trends that will shape information management for the foreseeable future. Those trends imply three major requirements for Impliance: (1) to be able to store, manage, and uniformly query all data, not just structured records; (2) to be able to scale out as the volume of this data grows; and (3) to be simple and robust in operation. We then describe four key ideas that are uniquely combined in Impliance to address these requirements, namely the ideas of: (a) integrating software and off-the-shelf hardware into a generic information appliance; (b) automatically discovering, organizing, and managing all data - unstructured as well as structured - in a uniform way; (c) achieving scale-out by exploiting simple, massive parallel processing, and (d) virtualizing compute and storage resources to unify, simplify, and streamline the management of Impliance. Impliance is an ambitious, long-term effort to define simpler, more robust, and more scalable information systems for tomorrow's enterprises.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

An automated ETL for online datasets

While using online datasets for machine learning is commonplace today, the quality of these datasets impacts on the performance of prediction algorithms. One method for improving the semantics of new data sources is to map these sources to a common data model or ontology. While semantic and structural heterogeneities must still be resolved, this provides a well established approach to providing clean datasets, suitable for machine learning and analysis. However, when there is a requirement for a close to real time usage of online data, a method for dynamic Extract-Transform-Load of new sources data must be developed. In this work, we present a framework for integrating online and enterprise data sources, in close to real time, to provide datasets for machine learning and predictive algorithms. An exhaustive evaluation compares a human built data transformation process with our system’s machine generated ETL process, with very favourable results, illustrating the value and impact of an automated approach

An automated ETL for online datasets

While using online datasets for machine learning is commonplace today, the quality of these datasets impacts on the performance of prediction algorithms. One method for improving the semantics of new data sources is to map these sources to a common data model or ontology. While semantic and structural heterogeneities must still be resolved, this provides a well established approach to providing clean datasets, suitable for machine learning and analysis. However, when there is a requirement for a close to real time usage of online data, a method for dynamic Extract-Transform-Load of new sources data must be developed. In this work, we present a framework for integrating online and enterprise data sources, in close to real time, to provide datasets for machine learning and predictive algorithms. An exhaustive evaluation compares a human built data transformation process with our system’s machine generated ETL process, with very favourable results, illustrating the value and impact of an automated approach

An automated ETL for online datasets

While using online datasets for machine learning is commonplace today, the quality of these datasets impacts on the performance of prediction algorithms. One method for improving the semantics of new data sources is to map these sources to a common data model or ontology. While semantic and structural heterogeneities must still be resolved, this provides a well established approach to providing clean datasets, suitable for machine learning and analysis. However, when there is a requirement for a close to real time usage of online data, a method for dynamic Extract-Transform-Load of new sources data must be developed. In this work, we present a framework for integrating online and enterprise data sources, in close to real time, to provide datasets for machine learning and predictive algorithms. An exhaustive evaluation compares a human built data transformation process with our system’s machine generated ETL process, with very favourable results, illustrating the value and impact of an automated approach

A rapid prototyping/artificial intelligence approach to space station-era information management and access

Applications of rapid prototyping and Artificial Intelligence techniques to problems associated with Space Station-era information management systems are described. In particular, the work is centered on issues related to: (1) intelligent man-machine interfaces applied to scientific data user support, and (2) the requirement that intelligent information management systems (IIMS) be able to efficiently process metadata updates concerning types of data handled. The advanced IIMS represents functional capabilities driven almost entirely by the needs of potential users. Space Station-era scientific data projected to be generated is likely to be significantly greater than data currently processed and analyzed. Information about scientific data must be presented clearly, concisely, and with support features to allow users at all levels of expertise efficient and cost-effective data access. Additionally, mechanisms for allowing more efficient IIMS metadata update processes must be addressed. The work reported covers the following IIMS design aspects: IIMS data and metadata modeling, including the automatic updating of IIMS-contained metadata, IIMS user-system interface considerations, including significant problems associated with remote access, user profiles, and on-line tutorial capabilities, and development of an IIMS query and browse facility, including the capability to deal with spatial information. A working prototype has been developed and is being enhanced

Metadata-driven data integration

Cotutela: Universitat Politècnica de Catalunya i Université Libre de Bruxelles, IT4BI-DC programme for the joint Ph.D. degree in computer science.Data has an undoubtable impact on society. Storing and processing large amounts of available data is currently one of the key success factors for an organization. Nonetheless, we are recently witnessing a change represented by huge and heterogeneous amounts of data. Indeed, 90% of the data in the world has been generated in the last two years. Thus, in order to carry on these data exploitation tasks, organizations must first perform data integration combining data from multiple sources to yield a unified view over them. Yet, the integration of massive and heterogeneous amounts of data requires revisiting the traditional integration assumptions to cope with the new requirements posed by such data-intensive settings. This PhD thesis aims to provide a novel framework for data integration in the context of data-intensive ecosystems, which entails dealing with vast amounts of heterogeneous data, from multiple sources and in their original format. To this end, we advocate for an integration process consisting of sequential activities governed by a semantic layer, implemented via a shared repository of metadata. From an stewardship perspective, this activities are the deployment of a data integration architecture, followed by the population of such shared metadata. From a data consumption perspective, the activities are virtual and materialized data integration, the former an exploratory task and the latter a consolidation one. Following the proposed framework, we focus on providing contributions to each of the four activities. We begin proposing a software reference architecture for semantic-aware data-intensive systems. Such architecture serves as a blueprint to deploy a stack of systems, its core being the metadata repository. Next, we propose a graph-based metadata model as formalism for metadata management. We focus on supporting schema and data source evolution, a predominant factor on the heterogeneous sources at hand. For virtual integration, we propose query rewriting algorithms that rely on the previously proposed metadata model. We additionally consider semantic heterogeneities in the data sources, which the proposed algorithms are capable of automatically resolving. Finally, the thesis focuses on the materialized integration activity, and to this end, proposes a method to select intermediate results to materialize in data-intensive flows. Overall, the results of this thesis serve as contribution to the field of data integration in contemporary data-intensive ecosystems.Les dades tenen un impacte indubtable en la societat. La capacitat d’emmagatzemar i processar grans quantitats de dades disponibles és avui en dia un dels factors claus per l’èxit d’una organització. No obstant, avui en dia estem presenciant un canvi representat per grans volums de dades heterogenis. En efecte, el 90% de les dades mundials han sigut generades en els últims dos anys. Per tal de dur a terme aquestes tasques d’explotació de dades, les organitzacions primer han de realitzar una integració de les dades, combinantles a partir de diferents fonts amb l’objectiu de tenir-ne una vista unificada d’elles. Per això, aquest fet requereix reconsiderar les assumpcions tradicionals en integració amb l’objectiu de lidiar amb els requisits imposats per aquests sistemes de tractament massiu de dades. Aquesta tesi doctoral té com a objectiu proporcional un nou marc de treball per a la integració de dades en el context de sistemes de tractament massiu de dades, el qual implica lidiar amb una gran quantitat de dades heterogènies, provinents de múltiples fonts i en el seu format original. Per això, proposem un procés d’integració compost d’una seqüència d’activitats governades per una capa semàntica, la qual és implementada a partir d’un repositori de metadades compartides. Des d’una perspectiva d’administració, aquestes activitats són el desplegament d’una arquitectura d’integració de dades, seguit per la inserció d’aquestes metadades compartides. Des d’una perspectiva de consum de dades, les activitats són la integració virtual i materialització de les dades, la primera sent una tasca exploratòria i la segona una de consolidació. Seguint el marc de treball proposat, ens centrem en proporcionar contribucions a cada una de les quatre activitats. La tesi inicia proposant una arquitectura de referència de software per a sistemes de tractament massiu de dades amb coneixement semàntic. Aquesta arquitectura serveix com a planell per a desplegar un conjunt de sistemes, sent el repositori de metadades al seu nucli. Posteriorment, proposem un model basat en grafs per a la gestió de metadades. Concretament, ens centrem en donar suport a l’evolució d’esquemes i fonts de dades, un dels factors predominants en les fonts de dades heterogènies considerades. Per a l’integració virtual, proposem algorismes de rescriptura de consultes que usen el model de metadades previament proposat. Com a afegitó, considerem heterogeneïtat semàntica en les fonts de dades, les quals els algorismes de rescriptura poden resoldre automàticament. Finalment, la tesi es centra en l’activitat d’integració materialitzada. Per això proposa un mètode per a seleccionar els resultats intermedis a materialitzar un fluxes de tractament intensiu de dades. En general, els resultats d’aquesta tesi serveixen com a contribució al camp d’integració de dades en els ecosistemes de tractament massiu de dades contemporanisLes données ont un impact indéniable sur la société. Le stockage et le traitement de grandes quantités de données disponibles constituent actuellement l’un des facteurs clés de succès d’une entreprise. Néanmoins, nous assistons récemment à un changement représenté par des quantités de données massives et hétérogènes. En effet, 90% des données dans le monde ont été générées au cours des deux dernières années. Ainsi, pour mener à bien ces tâches d’exploitation des données, les organisations doivent d’abord réaliser une intégration des données en combinant des données provenant de sources multiples pour obtenir une vue unifiée de ces dernières. Cependant, l’intégration de quantités de données massives et hétérogènes nécessite de revoir les hypothèses d’intégration traditionnelles afin de faire face aux nouvelles exigences posées par les systèmes de gestion de données massives. Cette thèse de doctorat a pour objectif de fournir un nouveau cadre pour l’intégration de données dans le contexte d’écosystèmes à forte intensité de données, ce qui implique de traiter de grandes quantités de données hétérogènes, provenant de sources multiples et dans leur format d’origine. À cette fin, nous préconisons un processus d’intégration constitué d’activités séquentielles régies par une couche sémantique, mise en oeuvre via un dépôt partagé de métadonnées. Du point de vue de la gestion, ces activités consistent à déployer une architecture d’intégration de données, suivies de la population de métadonnées partagées. Du point de vue de la consommation de données, les activités sont l’intégration de données virtuelle et matérialisée, la première étant une tâche exploratoire et la seconde, une tâche de consolidation. Conformément au cadre proposé, nous nous attachons à fournir des contributions à chacune des quatre activités. Nous commençons par proposer une architecture logicielle de référence pour les systèmes de gestion de données massives et à connaissance sémantique. Une telle architecture consiste en un schéma directeur pour le déploiement d’une pile de systèmes, le dépôt de métadonnées étant son composant principal. Ensuite, nous proposons un modèle de métadonnées basé sur des graphes comme formalisme pour la gestion des métadonnées. Nous mettons l’accent sur la prise en charge de l’évolution des schémas et des sources de données, facteur prédominant des sources hétérogènes sous-jacentes. Pour l’intégration virtuelle, nous proposons des algorithmes de réécriture de requêtes qui s’appuient sur le modèle de métadonnées proposé précédemment. Nous considérons en outre les hétérogénéités sémantiques dans les sources de données, que les algorithmes proposés sont capables de résoudre automatiquement. Enfin, la thèse se concentre sur l’activité d’intégration matérialisée et propose à cette fin une méthode de sélection de résultats intermédiaires à matérialiser dans des flux des données massives. Dans l’ensemble, les résultats de cette thèse constituent une contribution au domaine de l’intégration des données dans les écosystèmes contemporains de gestion de données massivesPostprint (published version

Organising interoperability information on highly dynamic and heterogeneous environments

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de ComputadoresThe “Internet of Things” is a dynamic global network infrastructure where physical and virtual “things” communicate and share information amongst themselves. Plug and Interoperate is an approach that allows heterogeneous “things” to plug (into data) and seamlessly exchange information within the environment. To allow that, Plug and Interoperate needs to have the comprehension about the existing interoperability information. For this, the interoperability information needs to be duly organised. However, and in the “Internet of Things”, this presents major challenges. First, it is difficult to index all interoperability information due to the “things” heterogeneity (many and different languages and formats) and due to the dynamics of the system (disparate things entering/leaving the environment at all times). Also, that the environment can be used with much different purposes, which hinders the way on how the interoperability information should be organised. So, an architecture of an Interoperability Repository System is presented, in order to organise all interoperability information in this kind of environments. The solution handles heterogeneous interoperability information and allows users to add a User Space to the repository in order to customise it to specific needs. It also provides a notification mechanism in order to notify users of new or updated interoperability information

Polyflow: a Polystore-compliant mechanism to provide interoperability to heterogeneous provenance graphs

Many scientific experiments are modeled as workflows. Workflows usually output massive amounts of data. To guarantee the reproducibility of workflows, they are usually orchestrated by Workflow Management Systems (WfMS), that capture provenance data. Provenance represents the lineage of a data fragment throughout its transformations by activities in a workflow. Provenance traces are usually represented as graphs. These graphs allows scientists to analyze and evaluate results produced by a workflow. However, each WfMS has a proprietary format for provenance and do it in different granularity levels. Therefore, in more complex scenarios in which the scientist needs to interpret provenance graphs generated by multiple WfMSs and workflows, a challenge arises. To first understand the research landscape, we conduct a Systematic Literature Mapping, assessing existing solutions under several different lenses. With a clearer understanding of the state of the art, we propose a tool called Polyflow, which is based on the concept of Polystore systems, integrating several databases of heterogeneous origin by adopting a global ProvONE schema. Polyflow allows scientists to query multiple provenance graphs in an integrated way. Polyflow was evaluated by experts using provenance data collected from real experiments that generate phylogenetic trees through workflows. The experiment results suggest that Polyflow is a viable solution for interoperating heterogeneous provenance data generated by different WfMSs, from both a usability and performance standpoint.Muitos experimentos científicos são modelados como workflows (fluxos de trabalho). Workflows produzem comumente um grande volume de dados. De forma a garantir a reprodutibilidade desses workflows, estes geralmente são orquestrados por Sistemas de Gerência de Workflows (SGWfs), garantindo que dados de proveniência sejam capturados. Dados de proveniência representam o histórico de derivação de um dado ao longo da execução do workflow. Assim, o histórico de derivação dos dados pode ser representado por meio de um grafo de proveniência. Este grafo possibilita aos cientistas analisarem e avaliarem resultados produzidos por um workflow. Todavia, cada SGWf tem seu formato proprietário de representação para dados de proveniência, e os armazenam em diferentes granularidades. Consequentemente, em cenários mais complexos em que um cientista precisa analisar de forma integrada grafos de proveniência gerados por múltiplos workflows, isso se torna desafiador. Primeiramente, para entender o campo de pesquisa, realizamos um Mapeamento Sistemático da Literatura, avaliando soluções existentes sob diferentes lentes. Com uma compreensão mais clara do atual estado da arte, propomos uma ferramenta chamada Polyflow, inspirada em conceitos de sistemas Polystore, possibilitando a integração de várias bases de dados heterogêneas por meio de uma interface de consulta única que utiliza o ProvONE como schema global. Polyflow permite que cientistas submetam consultas em múltiplos grafos de proveniência de maneira integrada. Polyflow foi avaliado em conjunto com especialistas usando dados de proveniência coletados de workflows reais que apoiam o estudo de geração de árvores filogenéticas. O resultado da avaliação mostrou a viabilidade do Polyflow para interoperar semanticamente dados de proveniência gerado por distintos SGWfs, tanto do ponto de vista de desempenho quanto de usabilidade