Consistency of annotations across genomes
Rex Chisholm, Pascale Gaudet, Donghui Li
One of the strengths of curating orthologous genes is to compare
the similarities and differences in gene product function in
different organisms. For example, a G protein can be involved in
jasmonic acid mediated signaling pathway in plants (TAIR:gene: 3355558), in sensory perception of taste in mouse (MGI:95781) and
in aggregation during fruiting body development in Dictyostelium
(dictyBase:DDB0185046). All those are part of the heterotrimeric G- protein complex on the plasma membrane, have GTPase activity and
activate a downstream effector, such as adenylate cyclase or
phospholipase C. The reference genome effort provides a great opportunity to
improve the quality of the annotations.
(- Should we develop a visualization tool (based on Mary's) where we could not only see all annotations, and also differences and similarities? )
Advantages
(1) Annotating genes from different organisms at the same time provides a great opportunity to improve the ontology
(2) Comparing all annotations could help identify mistakes; for example oxidoreductases enzymes used to be annotated to process = electron transfer; when comparing all annotations, those would stand out and could be verified and corrected when necessary.
(3) Establishing the most granular common annotations would help curators annotate genes for which there is no experimental information (by ISS) by providing an overview of the common function, process, component of all studied genes.
The most useful way to do this would be to coordinate the efforts of the different databases.
Possible ways to coordinate annotation efforts
- assign a curator for each gene. The curator would be responsible
for checking across all databases, provide missing information, and suggest corrections. Curators can claim some of the genes while they are curating them
- each database where the ortholog has experimental evidence would
participate in a coordinated effort to annotate their respective gene; compare and if the group decides that the annotations look good, notify other databases that ISS annotations can be made, and possibly suggest what those should be.
Retun to [July 10 Conference call agenda]