A Finite Model Theory for Biological Hypotheses
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Journal of Biomedical Informatics
Pathway knowledge base: An integrated pathway resource using BioPAX
Applied Ontology - Towards a Metaontology for the Biomedical Domain
Realism for scientific ontologies
Proceedings of the 2010 conference on Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS 2010)
Data model for scientific models and hypotheses
The evolution of conceptual modeling
Artificial Intelligence and Law
Using ontology databases for scalable query answering, inconsistency detection, and data integration
Journal of Intelligent Information Systems
Knowledge-based integrative framework for hypothesis formation in biochemical networks
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Evaluating scientific hypotheses using the SPARQL inferencing notation
ESWC'12 Proceedings of the 9th international conference on The Semantic Web: research and applications
Pathway knowledge base: An integrated pathway resource using BioPAX
Applied Ontology - Towards a Metaontology for the Biomedical Domain
A scientific hypothesis conceptual model
ER'12 Proceedings of the 2012 international conference on Advances in Conceptual Modeling
Research lattices: towards a scientific hypothesis data model
Proceedings of the 25th International Conference on Scientific and Statistical Database Management
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Motivation: Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered. Results: We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology and programs to perform hypothesis design and evaluation. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information. Availability: www.hybrow.org