Departmental Papers (CIS)

Date of this Version

August 2006

Document Type

Journal Article


Electronic version of an article published as Journal of Bioinformatics and Computational Biology, Volume 4, Issue 5 (October 2006), pp. 1069-1095.
Article DOI: © copyright World Scientific Publishing Company
Journal URL:


Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer.

Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data.

In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.


bioinformatics, querying biological resources, paths between sources, metadata and user's preferences



Date Posted: 01 February 2007

This document has been peer reviewed.