Querying Annotated Scientific Data Combining Object-Oriented View and Information Retrieval

Scientific data is available in a wide variety of formats, annotated, and stored in flat-files and relational or object-oriented databases. A large part of the work of scientists today consists in querying a scientific digital library, integrated view of remote or local heterogeneous data sources with advanced data analyzing and visualization tools. Scientific data servers and in particular the ones publicly available on the Web, usually provide information retrieval techniques to access data. A mediator or multi-database approach to integrating scientific data and analysis tools therefore requires building a database view of data sources only accessible through information retrieval techniques. In this paper we present an Object-Web Wrapper (OWW) based on an intermediate object view mechanism called search views mapping full-text retrieval accesses to attributes. The Object-Web Wrapper has been implemented as a server of the object-oriented multi-database system developed at Gene Logic Inc. To the best of our knowledge, the multi-database system extended with OWW is the only system that offers (1) an object view mechanism to represent data retrieved by R techniques, and (2) a user-friendly transparent way to express search conditions within OQL queries (or through OQL queries generated with the query editor facility) against Web data sources.

[1]  Christian Burks,et al.  Molecular Biology Database List , 1999, Nucleic Acids Res..

[2]  I-Min A Chen,et al.  An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools , 1995, Inf. Syst..

[3]  Surajit Chaudhuri,et al.  Join queries with external text sources: execution and optimization techniques , 1995, SIGMOD '95.

[4]  Thure Etzold,et al.  SRS - an indexing and retrieval tool for flat file data libraries , 1993, Comput. Appl. Biosci..

[5]  Carole A. Goble,et al.  TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources , 1998, ISMB.

[6]  Nelson Mendonça Mattos,et al.  Integrating SQL Databases with Content-Specific Search Engines , 1997, VLDB.

[7]  I-Min A. Chen,et al.  Exploring Heterogeneous Biological Databases: Tools and Applications , 1998, EDBT.

[8]  I-Min A. Chen,et al.  Constructing and maintaining scientific database views in the framework of the object-protocol model , 1997, Proceedings. Ninth International Conference on Scientific and Statistical Database Management (Cat. No.97TB100150).

[9]  William W. Cohen.  Integration of heterogeneous databases without common domains using queries based on textual similarity , 1998, SIGMOD '98.

[10]  Guido Moerkotte,et al.  Querying documents in object databases , 1997, International Journal on Digital Libraries.

[11]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[12]  Shahrokh Saeednia,et al.  How to maintain both privacy and authentication in digital libraries , 2000 .

[13]  Zoé Lacroix.  Object Views through Search Views of Web Datasources , 1999, ER.

[14]  Roy Goldman,et al.  WSQ/DSQ: a practical approach for combined querying of databases and the Web , 2000, SIGMOD 2000.