DictyBase, March 2010
Staff
PI: Rex Chisholm Annotators: Petra Fey, Pascale Gaudet, Robert Dodson (started September 2009) Developers: Siddhartha Basu, Yulia Bushmanova, Eric Just, (consultant)
All dictyBase staff contributes to GO activities. This is a total of 5 FTE positions. Of these we receive sufficient funding from the GO grant to support about 1.05 FTEs.
Annotation. Gene Ontology annotation is integral to the curation process at dictyBase. Annotation of gene products to GO terms is done concurrently with curation of literature, phenotypes, and sequences. All curators work to annotate gene products of the Dictyostelium genome. We import GOA annotations into dictyBase and incorporate them into our monthly gene association file.
Reference Genome Project. Pascale is manager for the Reference Genome project. All dictyBase curators annotate reference genome genes and are up-to-date with the selected orthologs. A paper describing the project has been published earlier this year: Mi et al 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. NAR Database issue [1]
Other dictyBase contributions to GO:
All dictyBase curators work to improve the GO with GO editors and other curators in the field, and contribute to discussion on the GO email list and Source Forge. Pascale is a member of the Reference Genome, AmiGO/web presence, GO Evidence Code and Ontology development working groups. In the course of the Reference Genome Project, Pascale works with Suzi Lewis, Kara Dolinski and Paul Thomas (Panther) to develop a tree-based orthology inference system for the Reference Genome project. Currently there is a lot of effort in the development of the software tool, PAINT that will be used to make the tree-based annotations.
Petra is a member of the Newsletter group, the OBO-Edit working group, and the Reference Genome annotation group.
Siddhartha is part of the Software group.
dictyBase is moving to the use of the Chado schema to store GO annotations. As part of this move we will be redesigning a new GO annotation tool. Sequencing of the genomes of several species related to Dictyostelium discoideum, including D. purpureum and D. citrinum is underway. dictyBase will facilitate the annotation of these genomes as their sequences become publicly available.