History of RDP

  University of Illinois at Urbana-Champaign Period

  The RDP arose out of research conducted by two University of Illinois at Urbana-Champaign (UIUC) faculty members, Carl R. Woese and Gary J. Olsen. Woese recognized that, due to rRNA's conserved sequence, ribosomal RNA could be used to elicit phylogenetic relationships between organisms. They foresaw that making a collection of rRNA sequences available would be useful to the research community and stimulate research in this area. Initial funding for the RDP was awarded in 1989 by the Biological Instrumentation and Resources Program of the National Science Foundation. Argonne National Laboratory first hosted the RDP ftp and public sites and on January 5, 1992, 471 16S rRNA sequences, many of which were generated in Woese's laboratory, were made available to the public in the first release of the RDP. The public sites were moved to UIUC for Release 3.0 in August 1993. NSF predominantly supported the RDP to 1997. As data were originally stored as flat files, additional funding to migrate to a commercial database management system was awarded jointly to Michigan State University (MSU) and UIUC in 1995. During the last 18 months of core NSF funding, discussions with MSU faculty at the Center for Microbial Ecology led to the relocation of the RDP to MSU.

  Michigan State University Period

  With dbms migration and collaboration between MSU and UIUC begun, official support of the RDP by the Center for Microbial Ecology at MSU started December 1997. The RDP Curator continued to physically work at UIUC but participated in planning meetings for the RDP's official move to MSU in 1998. The first data release and official announcement of the RDP-II WWW site occurred July 31, 1998.

For Relases 7.1 and 8.0, RDP-II staff members at MSU included Bonnie Maidak, responsible for curation and user support, and Jim Cole, who oversaw, and continues to oversee, the website, database and development. Other staff members (Tim Lilburn, Chuck Parker, and Paul Saxman) served as curatorial assistants, system administrators, and programmers. Bonnie and Chuck left the RDP-II before Release 8.1 appeared, although they contributed substantially to the Release.

Four MSU faculty members from the Departments of Microbiology (Jim Tiedje, Tom Schmidt, and George Garrity) and Computer Science (Sakti Pramanik) serve in an advisory role. The RDP-II is currently funded by the US Department of Energy (DOE).

  Complete web statistics on this public server are available. During the first year of operation, the new website served over 15,000 distinct hosts from over 40 countries and averaged over 26 M bytes of data transferred per day. In order to determine the needs and perceptions of its user community, in early 1999 the RDP-II solicited user comments via a user survey. Most users felt that RDP-II should devote more resources to prokaryotic small subunit sequences, and that RDP-II could improve by releasing data in a more timely manner. The survey questions can be seen online. Since the first published article describing the RDP in 1991 (Olsen et al., 1991a), eight additional articles describing the RDP have been published in the annual databases issue of Nucleic Acids Research. These nine articles have been cited 2,087 times in journals covering areas of research such as AIDS, bioinformatics, dairy science, environmental microbiology, fermentation bioengineering, gastroenterology, and veterinary medicine, to name just a few.

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