[Gramene] 'Not available' gene symbols

Chris Mungall cjm at berkeleybop.org
Fri Jul 10 14:50:46 EDT 2009


gene_association.gramene_oryza.gz contains 775 genes with symbol 'Not  
available'

The guidelines are a little unclear on this:
http://www.geneontology.org/GO.format.annotation.shtml

>     this field is mandatory, cardinality 1
>     The DB_Object_Symbol field should be a symbol that means  
> something to a biologist, wherever possible (a gene symbol, for  
> example). It is not an ID or an accession number (the second column,  
> DB_Object_ID, provides the unique identifier), although IDs can be  
> used in DB_Object_Symbol if there is no more biologically meaningful  
> symbol available (e.g., when an unnamed gene is annotated).

The policy for unnamed genes should be made clearer, with a  
recommendation to use the ID when the symbol is unavailable (my own  
preference would be to simply have the column empty but this would not  
be backwards compatible). We should also state that the symbol should  
strive to be unique within a species.

Can you change the 1498 lines your annotation file to use col2 rather  
than the 'Not available' string? Thanks.



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