[Go] [go] annotations for refgenomes

[Valerie Wood]

>
>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.
>
>
>  
>

hi Mike,

I see your point for teaching purposes, but doesn't   the inclusion of  
ND's help to show  more clearly the number of genes which have not been 
studied? It is the work of curators, but its aim is to show where there 
is no data available i.e. there is no research. Otherwise you don't know 
whether the absence of data in the graph is due to the lack of data or 
the lack of curation.

The fact that not all MODs have made all the possible ND annotations 
also makes its inclusion helpful to interpret of the data. You can see 
clearly in the graph where the ND data is included that for pombe and 
cerevisiae all genes have been looked at, because F,P and C bars are the 
same size. For other organisms they are different sizes which would 
indicate ND is not saturating (i.e there could be more biological 
knowledge but it hasn't been curated yet).

If the ND data was shown at the top of the bar, you could mentally 
include or exclude it. It is probably not so useful when combined with 
NAS,ND,IC,TAS, but we are all making best efforts to minimize the use of 
these codes, so I guess they will eventually disappear.

Coincidently the reviewers of our NRG review manuscript asked us to 
explain this annotation difference, and that some MODs use ND if there 
is ISS or IEA data available and some don't (between MODs) and how this 
affects GO usage.

Val









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