Emergent Semantics

Information and communication infrastructures underwent a rapid and extreme decentralization process over the past decade: From a world of statically and partially connected central servers rose an intricate web of millions of information sources loosely connecting one to another. The dynamism and relative autonomy of the individuals in the structure is now seen as a chance more than a threat to the stability and consistency of the overall system. New paradigms, like ad-hoc or peer-to-peer networks, even exacerbate this position by taking advantage of the liveliness and heterogeneity of their constituents in the creation of global, self-organizing structures. Today, we expect to witness the extension of this revolution with the wide adoption of meta-data standards like RDF or OWL underpinning the creation of a semantic web. Again, we hope for global properties to emerge from a multiplicity of pair-wise, local interactions, resulting eventually in a self-stabilizing semantic infrastructure. This paper represents an effort to summarize the conditions under which this revolution would take place as well as an attempt to underline its main properties, consequences and applications. Also, it proposes solutions to the main threads and limitations endangering the formation and proper functioning of such a large-scale, emergent semantic system.

Invited Paper II

Prof. Shamkant Navathe, Georgia Institute of Technology, USA

Shamkant Navathe is a professor and the head of the database research group at the College of Computing, Georgia Institute of Technology, Atlanta. He is well known for his work on database modeling, database conversion, database design, distributed database allocation, and database integration. He has worked with IBM and Siemens in their research divisions and has been a consultant to various companies including Digital, CCA, HP and Equifax. He was the General Co-chairman of the 1996 International VLDB (Very Large Data Base) conference in Bombay, India. He was also program co-chair of ACM SIGMOD 1985 International Conference and General Co-chair of the IFIP WG 2.6 Data Semantics Workshop in 1995. He was a member of the VLDB foundation and has been on the steering committees of several conferences. He has been an associate editor of ACM Computing Surveys, and IEEE Transactions on Knowledge and Data Engineering. He is also on the editorial boards of Information Systems and Distributed and Parallel Databases. He is an author of the book, Fundamentals of Database Systems, with R. Elmasri (Addison Wesley, Edition 4) - which is currently the leading database textbook worldwide. He also co-authored the book "Conceptual Design: An Entity Relationship Approach" (Addison Wesley, 1992) with Carlo Batini and Stefano Ceri.
   His current research interests include human genome data management, microarray data analysis, data and text mining, mobile databases and synchronization, engineering data management, intelligent information retrieval, and web-based database applications.
   Navathe holds a Ph.D. from the University of Michigan and has over 125 refereed publications.

Title: Genomic and Proteomic Databases and Applications: A Challenge for Database Technology
Co-author: M.D. Upen Patil
Abstract:

The biological science studies the phenomenon of life and encompasses an enormous variety of information. After the sequencing of the entire human genome, the field of genomics and proteomics has indeed come into limelight. The objective of Genomics is to undertake a systematic investigation of genomes while Proteomics deals with the quantitative measurement of protein expression. Data management of such highly variable complex biological phenomena now poses a challenge for database technology and includes data that ranges from research articles to complex metabolic pathways. Research advances in computational biology, molecular biology, genomic medicine and pharmacogenomics have now become critically dependent on what information such databases contain. It is not possible with the available technology of web links to get a complete and uniform picture of where science stands today on any one of these organisms unless a scientist spends many hours using search engines with some associated frustration. Metadata management, data interpretation, data integration, uniform interface creation, and visualization pose challenges with major opportunities for database research.

This paper starts off defining a number of essential biological concepts required to understand this complex field. We then survey the proliferation of genomic and proteomic databases around the world and describe the unique characteristics of biological data that make their management difficult. We highlight the pressing issues for further development of genomic and proteomic databases so they can support the type of applications they are intended for. Currently biological databases have ASN.1 (Abstract Syntax Notation 1) data format but relational DBMSs are getting more popular. RDBMSs generally fail to meet the semantic demands of irregular, incomplete, overlapping and ill-defined data, which is rampant in biology, and may be partly addressed by Object-oriented DBMSs. But the latter have failed to gain strength in query processing and scalability and lack commercial strength. This creates a void where database research may contribute substantially to this field. We point out a number of exciting areas for applications such as designer drugs and physician aids based on these databases and microarray data analysis. The shift in emphasis from data accumulation to data interpretation has already begun and will continue to expand. Further database research will go a long way to contribute to many public and private efforts in the broadly defined field of bioinformatics.