OpenII (openintegration.org) is a collaborative effort to create a suite of open-source tools for information integration (II). The project is leveraging the latest developments in II research to create a platform on which integration tools can be built and further research conducted. In addition to a scalable, extensible platform, OpenII includes industrial-strength components developed by MITRE, Google, UC-Irvine, and UC-Berkeley that interoperate through a common repository in order to solve II problems. Components of the toolkit have been successfully applied to several large-scale US government II challenges.

Large, dynamic, and ad-hoc organizations must frequently initiate data integration and sharing efforts with insufficient awareness of how organizational data sources are related. Decision makers need to reason about data model interactions much as they do about data instance interactions in OLAP: at multiple levels of granularity. We demonstrate an integrated environment for exploring schema similarity across multiple resolutions. Users visualize and interact with clusters of related schemas using a tool named Affinity. Within any cluster, users may drill-down to examine the extent and content of schema overlap. Further drill down enables users to explore fine-grained element-level correspondences between between two selected schemas.

This demonstration presents Galaxy, a schema manager that facilitates easy and correct data sharing among autonomous but related, evolving data sources. Galaxy reduces heterogeneity by helping database developers identify, reuse, customize, and advertise related schema components. The central idea is that as schemata are customized, Galaxy maintains a derivation graph, and exploits it for data exchange, discovery, and multi-database query over the "galaxy" of related data sources. Using a set of schemata from the biomedical domain, we demonstrate how Galaxy facilitates schema and data sharing.

Whereas strategies for discovering content on the surface web are commonplace, similar strategies for the private web are nonexistent. In this paper we first establish a formal framework for advertising the existence of private web resources that subsumes many existing summarization strategies based on succinct statistical summaries (which we call digests). We then investigate the tradeoff between the data owners' desires to minimize disclosure and the searchers' desires to minimize query error, demonstrating that our techniques are superior to k-anonymity. Finally, we show that our techniques for summarization do, in fact, make it possible to discover private web data resources.

Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, researchers must integrate these large and diverse data sets. This presents daunting informatic challenges such as representation of data that is suitable for computational inference (knowledge representation), and linking heterogeneous data sets (data integration). Fortunately, many of these challenges can be classified as data integration problems, and technologies exist in the area of data integration that may be applied to these challenges. In this paper, we discuss the opportunities of genomic medicine as well as identify the informatics challenges in this domain. We also review concepts and methodologies in the field of data integration. These data integration concepts and methodologies are then aligned with informatics challenges in genomic medicine and presented as potential solutions. We conclude this paper with challenges still not addressed in genomic medicine and gaps that remain in data integration research to facilitate genomic medicine.

For decades, researchers in knowledge representation (KR) have argued for and against various choices in KR formalisms, such as Rules, Frames, Semantic nets, and Formal logic. In this paper, we present a set of transformations that can be used to move knowledge across two fundamentally different KR formalisms: Frame-based systems and Relational database systems (RDBs). We also describe partial implementations of these transformations for a specific pair of such systems: Protégé and the Postgres RDB system.

The difficulty inherent in schema matching has led to the development of several generic match algorithms. We describe how we adapted general approaches to the specific task of aligning two ontologies of human anatomy, the Foundational Model of Anatomy and the GALEN Common Reference Model. Our approach consists of three phases: lexical, structural and hierarchical, which leverage different aspects of the ontologies as they are represented in a generic meta-model. Lexical matching identifies concepts with similar names. Structural matching identifies concepts whose neighbors are similar. Finally, hierarchical matching identifies concepts with similar descendants. We conclude by reporting on the lessons we learned.

Intuitively, data management and data integration tools are well-suited for exchanging information in a semantically meaningful way. Unfortunately, they suffer from two significant problems: They typically require a comprehensive schema design before they can be used to store or share information and they are difficult to extend because schema evolution is heavyweight and may break backward compatibility. As a result, many small-scale data sharing tasks are more easily facilitated by nondatabase-oriented tools that have little support for semantics. The goal of the peer data management system (PDMS) is to address this need: We propose the use of a decentralized, easily extensible data management architecture in which any user can contribute new data, schema information, or even mappings between other peers' schemes. PDMSs represent a natural step beyond data integration systems, replacing their single logical schema with an interlinked collection of semantic mappings between peers' individual schemas. This paper describes-several aspects of the Piazza PDMS, including the schema mediation formalism, query answering and optimization algorithms, and the relevance of PDMSs to the semantic Web.

The Semantic Web envisions a World Wide Web in which data is described with rich semantics and applications can pose complex queries. To this point, researchers have defined new languages for specifying meanings for concepts and developed techniques for reasoning about them, using RDF as the data model. To flourish, the Semantic Web needs to be able to accommodate the huge amounts of existing data and the applications operating on them. To achieve this, we are faced with two problems. First, most of the world's data is available not in RDF but in XML; XML and the applications consuming it rely not only on the domain structure of the data, but also on its document structure. Hence, to provide interoperability between such sources, we must map between both their domain structures and their document structures. Second, data management practitioners often prefer to exchange data through local point-to-point data translations, rather than mapping to common mediated schemas or ontologies.This paper describes the Piazza system, which addresses these challenges. Piazza offers a language for mediating between data sources on the Semantic Web, which maps both the domain structure and document structure. Piazza also enables interoperation of XML data with RDF data that is accompanied by rich OWL ontologies. Mappings in Piazza are provided at a local scale between small sets of nodes, and our query answering algorithm is able to chain sets mappings together to obtain relevant data from across the Piazza network. We also describe an implemented scenario in Piazza and the lessons we learned from it.