Biology Reference
In-Depth Information
towards
Arabidopsis thaliana
and
Oryza sativa.
The Fungal Proteome
Annotation Project (FPAP) focuses on the annotation of complete
fungal proteomes, concentrating on
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
as well as other model species such as
Neurospora crassa
and the human pathogens
Candida albicans
and
Emericella nidulans
. Bacterial and archaeal model organisms are anno-
tated as part of the HAMAP (High-quality Automated and Manual
Annotation of microbial Proteomes) project, which identifies proteins
that are part of well-conserved families and semiautomatically anno-
tates them based on manually created family rules. Manual annotation
efforts are also directed towards nonmammalian vertebrates (e.g.
zebrafish and
Xenopus
) and invertebrate species (e.g.
Drosophila
melanogaster
and
Caenorhabditis elegans
).
Until very recently,
D. discoideum
was not one of UniProt's priorities;
but when we decided to explore how a generalist data resource such as
UniProt could most effectively work in synergy with an MOD (such as
dictyBase),
D. discoideum
appeared as an optimal test case. Furthermore,
to work with the community of researchers trying to understand the par-
ticular and peculiar lifestyle of this fascinating organism seemed an entic-
ing project. This community is quite unique in its sociological aspects. Its
collaborative and altruistic spirit makes a refreshing contrast to the more
competitive atmosphere which is pervasive in larger communities working
with organisms that are deemed to be more important to the life sciences
research universe.
We therefore decided to work in close collaboration with the
dictyBase team to fully annotate all of the
D. discoideum
proteins and,
subsequently, bring them into Swiss-Prot. We bootstrapped such an
effort by organizing, in Geneva in February 2008, an annotation jam-
boree that brought together Swiss-Prot annotators from the SIB, EBI,
and PIR with dictyBase curators and some
D. discoideum
researchers.
Not only was the jamboree a complete success, but it also led us — as will
be later pointed out — to the unforeseen conclusion that
D. discoideum
is a good prototype for establishing rules to propagate annotation to
many uncharacterized eukaryotic organisms whose genome is or will
soon be available.
