No abstract

With the current explosion of information on the World Wide Web (WWW) a wealth of information on many different subjects has become available on-line. Numerous sources contain information that can be classified as semi-structured. At present, however, the only way to access the information is by browsing individual pages. We cannot query web documents in a database-like fashion based on their underlying structure. However, we can provide database-like querying for semi-structured WWW sources by building wrappers around these sources. We present an approach for semi-automatically generating such wrappers. The key idea is to exploit the formatting information in pages from the source to hypothesize the underlying structure of a page. From this structure the system generates a wrapper that facilitates querying of a source and possibly integrating it with other sources. We demonstrate the ease with which we are able to build wrappers for a number of internet sources in different domains using our implemented wrapper generation toolkit.

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery.

The Web is based on a browsing paradigm that makes it difficult to retrieve and integrate data from multiple sites. Today, the only way to do this is to build specialized applications, which are time-consuming to develop and difficult to maintain. We have addressed this problem by creating the technology and tools for rapidly constructing information agents that extract, query, and integrate data from web sources. Our approach is based on a uniform representation that makes it simple and efficient to integrate multiple sources. Instead of building specialized algorithms for handling web sources, we have developed methods for mapping web sources into this uniform representation. This approach builds on work from knowledge representation, databases, machine learning and automated planning. The resulting system, called Ariadne, makes it fast and easy to build new information agents that access existing web sources. Ariadne also makes it easy to maintain these agents and incorporate new sources as they become available.

We found that the Common Data Model from the OMOP met the broadest complement of CER objectives. Minimal information loss occurred in mapping data from institution-specific data warehouses onto the data models from the standards we assessed. However, to support certain scenarios, we found a need to enhance existing data dictionaries with local, institution-specific information.