XML Matchers: approaches and challenges

Schema Matching, i.e. the process of discovering semantic correspondences between concepts adopted in different data source schemas, has been a key topic in Database and Artificial Intelligence research areas for many years. In the past, it was largely investigated especially for classical database models (e.g., E/R schemas, relational databases, etc.). However, in the latest years, the widespread adoption of XML in the most disparate application fields pushed a growing number of researchers to design XML-specific Schema Matching approaches, called XML Matchers, aiming at finding semantic matchings between concepts defined in DTDs and XSDs. XML Matchers do not just take well-known techniques originally designed for other data models and apply them on DTDs/XSDs, but they exploit specific XML features (e.g., the hierarchical structure of a DTD/XSD) to improve the performance of the Schema Matching process. The design of XML Matchers is currently a well-established research area. The main goal of this paper is to provide a detailed description and classification of XML Matchers. We first describe to what extent the specificities of DTDs/XSDs impact on the Schema Matching task. Then we introduce a template, called XML Matcher Template, that describes the main components of an XML Matcher, their role and behavior. We illustrate how each of these components has been implemented in some popular XML Matchers. We consider our XML Matcher Template as the baseline for objectively comparing approaches that, at first glance, might appear as unrelated. The introduction of this template can be useful in the design of future XML Matchers. Finally, we analyze commercial tools implementing XML Matchers and introduce two challenging issues strictly related to this topic, namely XML source clustering and uncertainty management in XML Matchers.Comment: 34 pages, 8 tables, 7 figure

Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources

On the Foundations of Data Interoperability and Semantic Search on the Web

This dissertation studies the problem of facilitating semantic search across disparate ontologies that are developed by different organizations. There is tremendous potential in enabling users to search independent ontologies and discover knowledge in a serendipitous fashion, i.e., often completely unintended by the developers of the ontologies. The main difficulty with such search is that users generally do not have any control over the naming conventions and content of the ontologies. Thus terms must be appropriately mapped across ontologies based on their meaning. The meaning-based search of data is referred to as semantic search, and its facilitation (aka semantic interoperability) then requires mapping between ontologies. In relational databases, searching across organizational boundaries currently involves the difficult task of setting up a rigid information integration system. Linked Data representations more flexibly tackle the problem of searching across organizational boundaries on the Web. However, there exists no consensus on how ontology mapping should be performed for this scenario, and the problem is open. We lay out the foundations of semantic search on the Web of Data by comparing it to keyword search in the relational model and by providing effective mechanisms to facilitate data interoperability across organizational boundaries. We identify two sharply distinct goals for ontology mapping based on real-world use cases. These goals are: (i) ontology development, and (ii) facilitating interoperability. We systematically analyze these goals, side-by-side, and contrast them. Our analysis demonstrates the implications of the goals on how to perform ontology mapping and how to represent the mappings. We rigorously compare facilitating interoperability between ontologies to information integration in databases. Based on the comparison, class matching is emphasized as a critical part of facilitating interoperability. For class matching, various class similarity metrics are formalized and an algorithm that utilizes these metrics is designed. We also experimentally evaluate the effectiveness of the class similarity metrics on real-world ontologies. In order to encode the correspondences between ontologies for interoperability, we develop a novel W3C-compliant representation, named skeleton

Data Warehousing Scenarios for Model Management

Model management is a framework for supporting meta-data related applications where models and mappings are manipulated as first class objects using operations such as Match, Merge, ApplyFunction, and Compose. To demonstrate the approach, we show how to use model management in two scenarios related to loading data warehouses. The case study illustrates the value of model management as a methodology for approaching meta-data related problems. It also helps clarify the required semantics of key operations. These detailed scenarios provide evidence that generic model management is useful and, very likely, implementable

Supporting Tools for Automated Generation and Visual Editing of Relational-to-Ontology Mappings

La integració de dades amb formats heterogenis i de diversos dominis mitjançant tecnologies de la web semàntica permet solucionar la seva disparitat estructural i semàntica. L'accés a dades basat en ontologies (OBDA, en anglès) és una solució integral que es basa en l'ús d'ontologies com esquemes mediadors i el mapatge entre les dades i les ontologies per facilitar la consulta de les fonts de dades. No obstant això, una de les principals barreres que pot dificultar més l'adopció de OBDA és la manca d'eines per donar suport a la creació de mapatges entre dades i ontologies. L'objectiu d'aquesta investigació ha estat desenvolupar noves eines que permetin als experts sense coneixements d'ontologies la creació de mapatges entre dades i ontologies. Amb aquesta finalitat, s'han dut a terme dues línies de treball: la generació automàtica de mapatges entre dades relacionals i ontologies i l'edició dels mapatges a través de la seva representació visual. Les eines actualment disponibles per automatitzar la generació de mapatges estan lluny de proporcionar una solució completa, ja que es basen en els esquemes relacionals i amb prou feines tenen en compte els continguts de la font de dades relacional i les característiques de l'ontologia. No obstant això, les dades poden contenir relacions ocultes que poden ajudar a la generació de mapatges. Per superar aquesta limitació, hem desenvolupat AutoMap4OBDA, un sistema que genera automàticament mapatges R2RML a partir de l'anàlisi dels continguts de la font relacional i tenint en compte les característiques de l'ontologia. El sistema fa servir una tècnica d'aprenentatge d'ontologies per inferir jerarquies de classes, selecciona les mètriques de similitud de cadenes en base a les etiquetes de les ontologies i analitza les estructures de grafs per generar els mapatges a partir de l'estructura de l'ontologia. La representació visual per mitjà d'interfícies intuïtives pot ajudar els usuaris sense coneixements tècnics a establir mapatges entre una font relacional i una ontologia. No obstant això, les eines existents per a l'edició visual de mapatges mostren algunes limitacions. En particular, la representació visual de mapatges no contempla les estructures de la font relacional i de l'ontologia de forma conjunta. Per superar aquest inconvenient, hem desenvolupat Map-On, un entorn visual web per a l'edició manual de mapatges. AutoMap4OBDA ha demostrat que supera les prestacions de les solucions existents per a la generació de mapatges. Map-On s'ha aplicat en projectes d'investigació per verificar la seva eficàcia en la gestió de mapatges.La integración de datos con formatos heterogéneos y de diversos dominios mediante tecnologías de la Web Semántica permite solventar su disparidad estructural y semántica. El acceso a datos basado en ontologías (OBDA, en inglés) es una solución integral que se basa en el uso de ontologías como esquemas mediadores y mapeos entre los datos y las ontologías para facilitar la consulta de las fuentes de datos. Sin embargo, una de las principales barreras que puede dificultar más la adopción de OBDA es la falta de herramientas para apoyar la creación de mapeos entre datos y ontologías. El objetivo de esta investigación ha sido desarrollar nuevas herramientas que permitan a expertos sin conocimientos de ontologías la creación de mapeos entre datos y ontologías. Con este fin, se han llevado a cabo dos líneas de trabajo: la generación automática de mapeos entre datos relacionales y ontologías y la edición de los mapeos a través de su representación visual. Las herramientas actualmente disponibles para automatizar la generación de mapeos están lejos de proporcionar una solución completa, ya que se basan en los esquemas relacionales y apenas tienen en cuenta los contenidos de la fuente de datos relacional y las características de la ontología. Sin embargo, los datos pueden contener relaciones ocultas que pueden ayudar a la generación de mapeos. Para superar esta limitación, hemos desarrollado AutoMap4OBDA, un sistema que genera automáticamente mapeos R2RML a partir del análisis de los contenidos de la fuente relacional y teniendo en cuenta las características de la ontología. El sistema emplea una técnica de aprendizaje de ontologías para inferir jerarquías de clases, selecciona las métricas de similitud de cadenas en base a las etiquetas de las ontologías y analiza las estructuras de grafos para generar los mapeos a partir de la estructura de la ontología. La representación visual por medio de interfaces intuitivas puede ayudar a los usuarios sin conocimientos técnicos a establecer mapeos entre una fuente relacional y una ontología. Sin embargo, las herramientas existentes para la edición visual de mapeos muestran algunas limitaciones. En particular, la representación de mapeos no contempla las estructuras de la fuente relacional y de la ontología de forma conjunta. Para superar este inconveniente, hemos desarrollado Map-On, un entorno visual web para la edición manual de mapeos. AutoMap4OBDA ha demostrado que supera las prestaciones de las soluciones existentes para la generación de mapeos. Map-On se ha aplicado en proyectos de investigación para verificar su eficacia en la gestión de mapeos.Integration of data from heterogeneous formats and domains based on Semantic Web technologies enables us to solve their structural and semantic heterogeneity. Ontology-based data access (OBDA) is a comprehensive solution which relies on the use of ontologies as mediator schemas and relational-to-ontology mappings to facilitate data source querying. However, one of the greatest obstacles in the adoption of OBDA is the lack of tools to support the creation of mappings between physically stored data and ontologies. The objective of this research has been to develop new tools that allow non-ontology experts to create relational-to-ontology mappings. For this purpose, two lines of work have been carried out: the automated generation of relational-to-ontology mappings, and visual support for mapping editing. The tools currently available to automate the generation of mappings are far from providing a complete solution, since they rely on relational schemas and barely take into account the contents of the relational data source and features of the ontology. However, the data may contain hidden relationships that can help in the process of mapping generation. To overcome this limitation, we have developed AutoMap4OBDA, a system that automatically generates R2RML mappings from the analysis of the contents of the relational source and takes into account the characteristics of ontology. The system employs an ontology learning technique to infer class hierarchies, selects the string similarity metric based on the labels of ontologies, and analyses the graph structures to generate the mappings from the structure of the ontology. The visual representation through intuitive interfaces can help non-technical users to establish mappings between a relational source and an ontology. However, existing tools for visual editing of mappings show somewhat limitations. In particular, the visual representation of mapping does not embrace the structure of the relational source and the ontology at the same time. To overcome this problem, we have developed Map-On, a visual web environment for the manual editing of mappings. AutoMap4OBDA has been shown to outperform existing solutions in the generation of mappings. Map-On has been applied in research projects to verify its effectiveness in managing mappings