Integrating bioinformatic data sources over the SFSU ER design tools XML databus

ABSTRACT

The SFSU ER Design Tools were developed to support database design and data integration over multiple implementation data models. These tools allow users to enter and view Entity Relationship (ER) schemas and to translate ER schemas into a variety of equivalent implementation schemas, including Relational (ANSI SQL2), Object Oriented (ODMG 3.0), Spreadsheet (Universal Relation with associated functional dependencies) and W3C XML DTD. In addition, for each implementation data model, the Tools generate DDL statements to create a database, as well as simple JDBC/ODBC based code to dump stored data into an XML file and to load data from an XML file into a database. Data can be transferred from one data store to another over an HTTP based XML Databus. In this paper we describe the design and implementation of our XML Databus using Web Services, as well as a new strategy to support integration of bioinformatics data sets. We first manually identify semantically equivalent attributes in both schemas, then automatically join the corresponding data sets into a single integrated collection of XML formatted data. Our software is operational, and preliminary performance measurements over DTD and data downloaded from the NIH-NCBI Web site show that our strategy is feasible for moderately sized data sets.

REFERENCES

• 1: S. Vincent, Heterogeneous Data Transfer Using Web Services. M.S. Project Report. SFSU Computer Science Department Technical Report: SFSU_CS_TR_05_05 (2005).
• 2: S. Prasad, a Web Service Implementation of the ER Design Tool. M.S. Project Report. SFSU Computer Science Department Technical Report: SFSU_CS_TR_05_06 (2005).
• 3: Raghu Ramakrishnan , Johannes Gehrke, Database Management Systems, McGraw-Hill Science/Engineering/Math, 2002
• 4: Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval, Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering, p.57, May 19-21, 2004
• 5: S. B. Davidson , J. Crabtree , B. P. Brunk , J. Schug , V. Tannen , G. C. Overton , C. J. Stoeckert, Jr., K2/Kleisli and GUS: experiments in integrated access to genomic data sources, IBM Systems Journal, v.40 n.2, p.512-531, February 2001
• 6: T. Y. Jen, using XSLT to Translate NIH XML Data Files into ER Tools XML Data Files. M.S. Project Report. SFSU Computer Science Department Technical Report: SFSU_CS_TR_04_40 (2004).
• 7: E. Armstrong, Working with XML_ The Java API for XML Processing (JAXP) Tutorial. Date retrieved: 11/09/2006. http://java.sun.com/WebServices/jaxp/dist/1.1/docs/tutorial/index.html
• 8: Kim Topley, Java Web Services in a Nutshell, O'Reilly & Associates, Inc., Sebastopol, CA, 2003
• 9: E. Armstrong, J. Ball, et al, the J2EE#8482; 1.4 Tutorial (2005). http://java.sun.com/j2ee/1.4/docs/tutorial/doc/
• 10: D. Webber, D. and A. Dutton, Understanding ebXML, UDDI, XML/EDI (2000) http://www.xml.org/xml/feature_articles/2000_1107_miller.shtml
• 11: Web Services. Apple Computer, Inc (2002).
• 12: Yan Liu, Web Services Joins Using ER Design Tool XML Databus, M.S. Project Report. SFSU Computer Science Department Technical Report: SFSU_CS_TR_06_09 (2006).
• 13: SFSU ER Design Tools Web Site: https://dbsgrad.sfsu.edu/~erdesigntools

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.2 DATABASE MANAGEMENT
      H.2.1 Logical Design

General Terms:
Algorithms, Design, Measurement, Standardization

Keywords:
Web services data integration, distributed query processing, join processing, schema integration