DILS '09 Proceedings of the 6th International Workshop on Data Integration in the Life Sciences
On-the-Fly Integration and Ad Hoc Querying of Life Sciences Databases Using LifeDB
DEXA '09 Proceedings of the 20th International Conference on Database and Expert Systems Applications
OntoMatch: a monotonically improving schema matching system for autonomous data integration
IRI'09 Proceedings of the 10th IEEE international conference on Information Reuse & Integration
Ontology guided autonomous label assignment in wrapper induced tables with missing column names
IRI'09 Proceedings of the 10th IEEE international conference on Information Reuse & Integration
Wikipedia driven autonomous label assignment in wrapper induced tables with missing column names
Proceedings of the 2010 ACM Symposium on Applied Computing
Data integration systems for scientific applications
OTM'10 Proceedings of the 2010 international conference on On the move to meaningful internet systems
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Scientific workflows in Life Sciences are usually complex, and use many online databases, analysis tools, publication repositories and customized computation intensive desktop software in a coherent manner to respond to investigative queries. These investigative queries are generally ad hoc, ill-formed, and often, used only once to test a single hypothesis. In such cases, developing customized workflows becomes a major undertaking, rendering the effort truly expensive, prohibitive and resource intensive. Such high development costs often act as deterrents to many interesting queries and promising on-time scientific discoveries. In this paper, we introduce a new query language that combines workflow features for scientific applications, called BioFlow, that exploits many recent developments in internet communication, databases, wrapper and mediator technologies, ontology, and data integration. BioFlow is a declarative language that abstracts these features to help hide most procedural aspects of mediation, data integration, communication protocols, data extraction and workflow details. We will demonstrate that fairly complex workflows can be effortlessly and declaratively expressed in BioFlow in an ad hoc fashion at minimal costs. We also report a prototype implementation of BioFlow in Windows VB .NET that includes most of its powerful and representative features as proof of feasibility of our proposal.