RIBOWEB: Linking Structural Computations to a

Knowledge Base of Published Experimental Data

Richard O. Chen, Ramon Felciano & Russ B. Altman

Section on Medical Informatics, Stanford University, MSOB X-215

Stanford, CA, USA, 94305-5479, Tel: (415)725-3394, fax: (415) 725-7944

{rchen, felciano, altman}@smi.stanford.edu

Abstract

The world wide web (WWW) has become critical for storing and disseminating biological data. It offers an additional opportunity, however, to support distributed computation and sharing of results. Currently, computational analysis tools are often separated from the data in a manner that makes iterative hypothesis testing cumbersome. We hypothesize that the cycle of scientific reasoning (using data to build models, and evaluating models in light of data) can be facilitated with resources that link computations with semantic models of the data. RIBOWEB is an online knowledge-based resource that supports the creation of three-dimensional models of the 30S ribosomal subunit. It has three components: (I) a knowledge base containing representations of the essential physical components and published structural data, (II) computational modules that use the knowledge base to build or analyze structural models, and (III) a web-based user interface that supports multiple users, sessions and computations. We have built a prototype of RIBOWEB, and have used it to refine a rough model of the central domain of the 30S subunit from E. coli. Using a standard WWW browser client to compute the initial refinement, we identified a subset of problematic constraints, recomputed the model with modified constraints, displayed the resulting 3D structure, and assessed the degree to which experimental constraints were satisfied. We validated the model by computing its root mean squared distance from previously reported models, and by evaluating its ability to satisfy experimental constraints not used in the refinement procedure. Our results suggest that sophisticated and integrated computational capabilities can be delivered to biologists using this simple three-component architecture.

This page under construction. It will point to a demo version of the Riboweb project. Other info can also be found here. It will also point to our previous efforts at building models of the 30S subunit.