In late 2001 the BioMOBY project was initiated with the goal of producing an open-source, simple, extensible platform to enable the discovery, representation, integration, and retrieval of biological data from widely disparate data hosts and analysis services. An early prototype, based on a web-services paradigm (MOBY-S), but using a novel ontology-aware registry system, was deployed and tested throughout 2002. Approximately 12 retrieval and analysis services were constructed spanning four institutions in Canada and the United States. The strengths and weaknesses of the prototype were evaluated and from this a more comprehensive and powerful API was written. The most significant changes affected data modeling, with the new API requiring strict adherence to a hierarchical object structure ontology. A compliant registry system and associated client/server side libraries were published in early 2003, and Proc Virt Conf Genom and Bioinf (3):17-27 Print ISSN 1547-383X Online ISSN 1547-7320 Copyright ' 2003. All Rights Reserved www.virtualgenomics.org Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not distributed for profit or commercial advantage. currently the registry is host to approximately 20 services in Canada, the United States, and Europe, and is expanding at the rate of approximately one service per day. In parallel with the web-services based approach, a concurrent branch of the BioMOBY project (S-MOBY) was established to examine a semantic-web approach to biological data discovery and integration. We anticipate being able to compare these two approaches on identical problem-sets in 2004.