Biology Reference
In-Depth Information
experiments such as large-scale mutagenesis and microarray-based gene
expression studies deposit their data in dictyBase to be integrated and
distributed to the research community. Phenotypic data are represented
using a controlled vocabulary that describes the consequences of muta-
tions reported for that gene. This type of information is not available in
UniProtKB, since its mission is to concentrate on information obtained
at the protein level. Conversely, most MODs, including dictyBase, rely
on UniProtKB to provide protein-specific information. In addition,
UniProtKB provides family annotation across a wide spectrum of organ-
isms, which, by definition, is not part of the mission of MODs.
3. Conclusion: Status and Perspective
3.1. Status of Dictyostelium Annotation in Swiss-Prot
Release 14.0 of UniProt contains 2479 manually reviewed
D. discoideum
entries. In terms of their protein existence level, the
breakdown is as follows:
Evidence at protein level
368
Evidence at transcript level
302
Inferred from homology
1611
Predicted
194
Uncertain
6
3.2. Future of Dictyostelium Annotation in Swiss-Prot
We plan to achieve the complete manual annotation of the
D. discoideum
,
proteome in the Swiss-Prot section of UniProtKB within 2 years (i.e. by
mid-2010). To ensure that we achieve this goal, we intend to make full
use of the synergy between the annotation efforts of dictyBase and those
of UniProt. We also plan to speed up the work by soliciting help from
the
Dictyostelium
research community. To increase the percentage of
proteins that have been confirmed at the protein level, we hope to convince
a number of proteomics facilities to run
D. discoideum
cellular extracts
through their protein identification pipelines. We will also import
