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Sixth ASM Conference on Candida and Candidiasis
CandidaDB World-Wide Web Server
During the Sixth ASM Conference on Candida and Candidiasis in January 2002, participants convened an informal workshop on annotation to ensure that the Candida research community has uniform genomic information. Participants included Christophe d'Enfert of Institut Pasteur and the European Consortium Galar Fungail; Jan Dungan, who works with Nina Agabian, at the University of California, San Francisco (UCSF); André Nantel, who works with Malcolm Whiteway of the National Research Council in Montreal, Quebec, Canada; Mike Lorenz, who works with Gerald Fink at the Massachusetts Insisitute of Technology, Cambridge; Diane Inglis, who works with Alexander Johnson at UCSF; Maria Costanzo of Proteome/Incyte in Beverly, Mass.; Nicole Hauser, who works with Steffen Rupp in Fraunhoffer IGB, Stuttgart, Germany; Eric Bensen, who works with Judith Berman at the University of Minnesota, St. Paul; and Kara Dolinski, who represented the Saccharomyces Genome Database at Stanford University, Stanford, Calif. The members of an ongoing annotation working group include Christophe d'Enfert, Jan Dungan, Andre Nantel, Mike Lorenz, Diane Inglis, M. Andrew Uhl, and Steffen Rupp.
The Candida annotations are based mainly on sequence Assembly 6 from the Stanford Genome Technology Center. To overcome the potential confusion if each group uses slightly different gene lists and deduced genetic relationships (e. g., linkage or allelism), those working in the field will need to better define genetic relationships as they are determined through ongoing experimental and informatics efforts. The main strategy for developing a uniform gene list and repository for new information consists of the following:
(i) Annotators will share current annotated data sets, which will be made publicly available even though complete agreement has not yet been achieved.
(ii) Six groups of annotators will attempt to resolve differences pertaining to particular fractions of the genes, with each group focusing on about 1,500 of the total 9,000, including Gene Ontology (GO) descriptions, and calling on experts to resolve questions about genetic relationships.
(iii) These efforts will involve exchanges of electronic information as well as a meeting scheduled for May 2002 to iron out details of rectifying gene lists. We are grateful to the Burroughs Wellcome Fund, the Wellcome Trust, and Pharmacia-Upjohn Corporation for supporting that meeting.
(iv) An advisory panel, whose members includes Neil Gow of the University of Aberdeen, Scotland, Dominique Sanglard of the University Hospital Lausanne, Switzerland, Judith Berman of the University of Minnesota, St. Paul, and Aaron Mitchell of Columbia University, New York, N.Y., will help to resolve difficult issues.
(v) The Saccharomyces Genomic Database will house the master gene list once the annotations are merged and will update and disseminate gene information, based on publicly available sequence information and input from the Candida research community. All members of the Candida research community are encouraged to update genetic and functional information at the Saccharomyces Genomic Database. Discordance concerning such issues as gene names will be resolved by the SGD in two steps. First, the interested parties will be urged to contact one another and resolve differences. Unresolved differences will be referred to the advisory panel, which may consult with interested parties and other members of the Candida research community.
The Candida research community owes a debt of gratitude to the Annotation Working Group for taking on a difficult and time-consuming task as a service. Our community also expresses the deepest gratitude to Stewart Scherer, whose advocacy for and analysis of the C. albicans genomic sequence has provided a pioneering contribution to our understanding of C. albicans biology. We are also grateful to those at the Stanford Genome Technology Center (SGTC) who have been directly responsible for the sequencing of the Candida genome, Ron Davis, director of SGTC, Nancy Federspiel, who supervised the sequencing project, and Ted Jones, who analyzed the genomic sequence and constructed Assembly 6, the basis for our current annotation. The community also thanks the National Institute of Dental Research and the Burroughs Wellcome Fund for supporting this work.
The progress documented here illustrates concretely that an ASM-sponsored conference can do much more than simply present the latest work a month before PubMed—a conference can be a forum for a research community that will soon provide a real and user-friendly benefit to all. Also, the fact that we could demonstrate widespread community support for our plan led directly and rapidly to successful fund-raising for the necessary follow-up meeting. In addition, two NIH Program Officers in attendance with interest in supporting these efforts now have contacts in the community, and could use the forum to focus their efforts and thoughts. Thus, the Candida research community is extremely grateful to ASM for their sponsorship of this conference.
Aaron P. Mitchell
Columbia University
New York, N.Y.
Email: webmaster@asmusa.org