Coordinating context building in heterogeneous information systems
Journal of Intelligent Information Systems - Special issue on next generation information technologies
Prototype implementation of the integrated genomic database
Computers and Biomedical Research
An overview of the object protocol model (OPM) and the OPM data management tools
Information Systems - Special issue: databases: their creation, management and utilization
Query reformulation for dynamic information integration
Journal of Intelligent Information Systems - Special issue on intelligent integration of information
InfoSleuth: agent-based semantic integration of information in open and dynamic environments
SIGMOD '97 Proceedings of the 1997 ACM SIGMOD international conference on Management of data
The Carnot Heterogeneous Database Project: Implemented Applications
Distributed and Parallel Databases
Managing semantic heterogeneity in databases: a theoretical prospective
PODS '97 Proceedings of the sixteenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systems
Reasoning in description logics
Principles of knowledge representation
Semantic interoperability in global information systems
ACM SIGMOD Record
Semantic integration of semistructured and structured data sources
ACM SIGMOD Record
Agent-based semantic interoperability in infosleuth
ACM SIGMOD Record
Distributed and Parallel Databases
Description Logics in Data Management
IEEE Transactions on Knowledge and Data Engineering
A Query Translation Scheme for Rapid Implementation of Wrappers
DOOD '95 Proceedings of the Fourth International Conference on Deductive and Object-Oriented Databases
Information Integration Using Logical Views
ICDT '97 Proceedings of the 6th International Conference on Database Theory
A Data Transformation System for Biological Data Sources
VLDB '95 Proceedings of the 21th International Conference on Very Large Data Bases
Querying Heterogeneous Information Sources Using Source Descriptions
VLDB '96 Proceedings of the 22th International Conference on Very Large Data Bases
Information Integration: Conceptual Modeling and Reasoning Support
COOPIS '98 Proceedings of the 3rd IFCIS International Conference on Cooperative Information Systems
Kleisli: Its Exchange Format, Supporting Tools, and an Application in Protein Interaction Extraction
BIBE '00 Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering
Integrating life sciences data-with a little Garlic
BIBE '00 Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering
COOPIS '96 Proceedings of the First IFCIS International Conference on Cooperative Information Systems
Query Processing in the TAMBIS Bioinformatics Source Integration System
SSDBM '99 Proceedings of the 11th International Conference on Scientific and Statistical Database Management
Guiding the User: An Ontology Driven Interface
UIDIS '99 Proceedings of the 1999 User Interfaces to Data Intensive Systems
Report on the EDBT'02 panel on scientific data integration
ACM SIGMOD Record
Registering Scientific Information Sources for Semantic Mediation
ER '02 Proceedings of the 21st International Conference on Conceptual Modeling
OilEd: A Reason-able Ontology Editor for the Semantic Web
KI '01 Proceedings of the Joint German/Austrian Conference on AI: Advances in Artificial Intelligence
Towards transparent access to multiple biological databanks
APBC '03 Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19
Rutabaga by any other name: extracting biological names
Journal of Biomedical Informatics - Special issue: Sublanguage
Estimating the quality of answers when querying over description logic ontologies
Data & Knowledge Engineering
Information integration: A new generation of information technology
IBM Systems Journal
Bioinformatics integration and agent technology
Journal of Biomedical Informatics
Information systems interoperability: What lies beneath?
ACM Transactions on Information Systems (TOIS)
Composing, optimizing, and executing plans for bioinformatics web services
The VLDB Journal — The International Journal on Very Large Data Bases
GRID '05 Proceedings of the 6th IEEE/ACM International Workshop on Grid Computing
A bilateral integrative health-care knowledge service mechanism based on 'MedGrid'
Computers in Biology and Medicine
Data Integration in the Life Sciences: Fun, Findings and Frustrations
DILS '08 Proceedings of the 5th international workshop on Data Integration in the Life Sciences
Grid Deployment of Legacy Bioinformatics Applications with Transparent Data Access
GRID '06 Proceedings of the 7th IEEE/ACM International Conference on Grid Computing
An ActOn-based semantic information service for Grids
Future Generation Computer Systems
Combining a high-throughput bioinformatics grid and bioinformatics web services
GCCB'06 Proceedings of the 2006 international conference on Distributed, high-performance and grid computing in computational biology
Semantically processing parallel colour descriptions
Journal on data semantics X
Dynamic query optimisation: towards decentralised methods
International Journal of Intelligent Information and Database Systems
An ontology based approach to automating data integration in scientific workflows
Proceedings of the 7th International Conference on Frontiers of Information Technology
Future Generation Computer Systems
Bioinformatics data source integration based on semantic relationships across species
VDMB'06 Proceedings of the First international conference on Data Mining and Bioinformatics
Data access and integration in the ISPIDER proteomics grid
DILS'06 Proceedings of the Third international conference on Data Integration in the Life Sciences
Integrating and querying parallel leaf shape descriptions
ISWC'06 Proceedings of the 5th international conference on The Semantic Web
Querying a bioinformatic data sources registry with concept lattices
ICCS'05 Proceedings of the 13th international conference on Conceptual Structures: common Semantics for Sharing Knowledge
Semantic interoperation among data systems at a communication level
Journal on Data Semantics V
BioRegistry: a structured metadata repository for bioinformatic databases
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
OTM'06 Proceedings of the 2006 international conference on On the Move to Meaningful Internet Systems: AWeSOMe, CAMS, COMINF, IS, KSinBIT, MIOS-CIAO, MONET - Volume Part II
Learning layouts of biological datasets semi-automatically
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Semantic correspondence in federated life science data integration systems
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Cluster based integration of heterogeneous biological databases using the automed toolkit
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Ontology–Based representation and query colour descriptions from botanical documents
OTM'05 Proceedings of the 2005 OTM Confederated international conference on On the Move to Meaningful Internet Systems: CoopIS, COA, and ODBASE - Volume Part II
ADVIS'06 Proceedings of the 4th international conference on Advances in Information Systems
Semantic search components: a blueprint for effective query language interfaces
EKAW'06 Proceedings of the 15th international conference on Managing Knowledge in a World of Networks
Chapter 15: search computing and the life sciences
Search Computing
Hi-index | 0.00 |
This paper describes the Transparent Access to Multiple Bioinformatics Information Sources project, known as TAMBIS, in which a domain ontology for molecular biology and bioinformatics is used in a retrieval-based information integration system for biologists. The ontology, represented using a description logic and managed by a terminology server, is used both to drive a visual query interface and as a global schema against which complex intersource queries are expressed. These source-independent declarative queries are then rewritten into collections of ordered source-dependent queries for execution by a middleware layer. In bioinformatics, the majority of data sources are not databases but tools with limited accessible interfaces. The ontology helps manage the interoperation between these resources. The paper emphasizes the central role that is played by the ontology in the system. The project distinguishes itself from others in the following ways: the ontology, developed by a biologist, is substantial; the retrieval interface is sophisticated; the description logic is managed by a sophisticated terminology server. A full pilot application is available as a JavaTM applet integrating five sources concerned with proteins. This pilot is currently undergoing field trials with working biologists and is being used to answer real questions in biology, one of which is used as a case study throughout the paper.