Advanced querying interface for biochemical network databases
Proceedings of the 2010 ACM Symposium on Applied Computing
Attempt to design a bio-medical knowledge discovery system
International Journal of Bio-Inspired Computation
Analyzing metabolite measurements for automated prediction of underlying biological mechanisms
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
PathCase-SB: database-enabled tools for regulatory metabolic networks
ACM SIGBioinformatics Record
PathCase-MAW: An Online Metabolic Network Analysis Workbench
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Querying KEGG pathways in logic
International Journal of Data Mining and Bioinformatics
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Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation and queriability over the web is important to facilitate ongoing biological research. Results: In this article, we present the new features of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal detail. The new features include: (i) a web-based system with a new architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases, (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) two distinct querying capabilities: an advanced querying interface for computer savvy users, and built-in queries for ease of use, that can be issued directly from pathway visualizations and (iv) a pathway functionality analysis tool. PathCase is now available for three different datasets, namely, KEGG pathways data, sample pathways from the literature and BioCyc pathways for humans. Availability: Available online at http://nashua.case.edu/pathways Contact: pathcase@case.edu