[Go] [go] annotations for refgenomes

[Mike Cherry]

On Feb 28, 2008, at 3:47 AM, Judith Blake wrote:

> Mike,
>
> I'm a little confused.  I don't understand how this is constructed.   
> Does number of genes 'ISS' mean the number of genes annotated Only  
> with ISS?  or are the numbers cumulative.  For mouse, for example,  
> do you mean to say that ~ 8000 genes are annotated with IGC or RCA?   
> or that ~ 1000 genes are annotated with these codes in addition to  
> the other codes except IEA?
>
> Judy
>

Its not only.  There is a hierarchy used.  If a gp had IDA, ISS and  
IEA then only IDA is counted.  If ISS and IEA then ISS is counted.   
Here is my order of evidence I use for the graphs:

(IMP|IDA|IPI|IGI|IEP) > (ISS) > (IC|NR|ND|NAS|TAS) > (IGC|RCA) > (IEA)

I use the graph for a class I teach.  My point is to show how many  
annotations exist and general classes of experimental, and non- 
experimental, evidence known for an organism's gene products.

For the ND annotations I prefer not to include them.  For sure ND are  
in the GA files but in my opinion they don't help the students  
understand the research of the model organism.  This is about  
community research not about the work of the MODs.  Annotations to the  
root are "No Data".  My point is how much or how little  
experimentation has been done on a particular organism.  ND shows the  
work of the curators, but what the experimental community hasn't  
done.  Also not all MODs have filled in annotations to the root for  
all gene products.  In my slide before this graph I talk about how  
many genes are in each organism.

Because of evolution we have this beautiful connectedness in biology.   
We work on the particular systems that are most appropriate, more  
powerful, in exploring biology.

-Mike