[Biojava-dev] Annotation conversions

[Matthew Pocock]

Hi Len,

This is a recurring problem with key-value data - exactly what is the 
right key? This is one of the things that ontologies are meant to solve 
for us. However, I still haven't got the ruddy things to work yet. For 
now, CC or COMMENT are your best bet. You can decide upon a canonical 
key if you want, but currently you would have to do the work by hand of 
mapping to/from canonical. Perhaps a useful thing to do would be to draw 
up a document with canonicals and what they map to in different file 
formats.

Matthew

Len Trigg wrote:

>Hi folks,
>
>I'd like to add support for BioSQL's comment table to our binding, and
>am wondering about the best way to do it. It is obvious that the
>comments should just be annotations, my question is more about what key I
>should associate the comments with (and should look for when storing
>sequences in the database). 
>
>It seems that I could use either "CC" or "COMMENT" and the right thing
>would happen most of the time. However, it seems a bit silly to have
>to check for both types when persisting comments to the
>database. Should there be a "canonical" key that is used for
>comments. Then different I/O formats could just check for this one
>key, rather than having to do do things like this:
>
>GenbankFileFormer.java:322
>        else if (key.equals("CC") || key.equals("COMMENT")) {
>            ccb = new StringBuffer(sequenceBufferCreator("COMMENT    ", value));
>        }
> 
>
>The same also applies to any of the annotations that are shared
>between multiple output formats...
>
>Suggestions?
>
>
>Cheers,
>Len.
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