Information Extraction & Object Views

Information extraction consists in identifying classes of events and relationships between extracted instances of these classes. In general, extracted data usually fills slots in a template and is stored in tables. We propose to extend the usual approach to the use of an object database. Information extraction tools have a conceptual representation as schema components: concept classes, meta-concepts and attributes. The user expresses in his query a structure (target structure) which corresponds to his understanding of the domain and is used as a schema for the database. We use the object data model whose syntax matches both the user\u27s target structure and the conceptual representation of extracting capabilities. Query evaluation consists in first determining the schema of the database as expressed by the user, and secondly populating the database through methods invoking extraction tools on a given source of documents. In a third step, it returns the output of the query against the resulting database. The two first steps define an object view of the given source(s) as a materialized extension of the current schema (each refinement of a query may add more structure, and thus more extracted data) followed by a non-materialized projection. Our approach is user-oriented: the object representation of data provides the user with the flexibility of asking his query with his understanding of the domain, and object views are built on-the-fly according to the user\u27s organization of data. The modularity of the conceptual representation of extraction capabilities in a pool of schema components enables easy plug-in of new extracting tools

BIPASS: BioInformatics Pipeline Alternative Splicing Services

BioInformatics Pipeline Alternative Splicing Services (BIPASS) offer support to scientists interested in gathering information related to alternative splicing (AS) events. The service BIPAS–SpliceDB provides access to AS information that has been extracted a priori from various public databases and stored in a data warehouse. In contrast, the BIPAS–Align&Splice service allows scientists to submit their own sequences and genome to compute AS analysis results. BIPAS services offer various user-friendly ways to navigate through the results. AS results are organized at different conceptual levels (clusters and sequences), and are displayed in graphs or summarized in tables that can be downloaded in XML or text format. The two BIPAS services SpliceDB and Align&Splice are available online at http://bip.umiacs.umd.edu:8080/

SPROUTS: a database for the evaluation of protein stability upon point mutation

SPROUTS (Structural Prediction for pRotein fOlding UTility System) is a new database that provides access to various structural data sets and integrated functionalities not yet available to the community. The originality of the SPROUTS database is the ability to gain access to a variety of structural analyses at one place and with a strong interaction between them. SPROUTS currently combines data pertaining to 429 structures that capture representative folds and results related to the prediction of critical residues expected to belong to the folding nucleus: the MIR (Most Interacting Residues), the description of the structures in terms of modular fragments: the TEF (Tightened End Fragments), and the calculation at each position of the free energy change gradient upon mutation by one of the 19 amino acids. All database results can be displayed and downloaded in textual files and Excel spreadsheets and visualized on the protein structure. SPROUTS is a unique resource to access as well as visualize state-of-the-art characteristics of protein folding and analyse the effect of point mutations on protein structure. It is available at http://bioinformatics.eas.asu.edu/sprouts.html

Object Views through Search Views of Web datasources

. Web datasources usually allow a restricted access (through CGI calls) and their output consists of generated HTML documents. Unfortunately, in many cases the data they provide happen to be available only on the Web. In this paper, we describe a system based on a Web wrapper combined with an object multidatabase system that enables the user to query Web datasources as well as other datasources with an OQL-like query language. The approach is based on two successive views of the Web datasource: a search view characterizing its access and an object view extending the restricted search view with respect the extraction capabilities of the wrapper. Both views are non-materialized to provide the user with up-to-date data. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform Object Protocol Model (OPM) interfaces. 1 Introduction In each domain, accessing the relevant data, combining datasources and coping with their distribution..