[Biojava-dev] Annotation conversions

[Len Trigg]

Matthew Pocock wrote:
> 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.

I just had another look at this. These are the ones I've seen that
have simple one to one conversions. There may be more:

Embl      Genbank
CC        COMMENT
OS        SOURCE
OC        ORGANISM
KW        KEYWORDS
SV        VERSION
DE        DEFINITION
DT        MDAT

There's probably some type of accession field.

There's also OrganismParser.PROPERTY_ORGANISM that has bidirectional
conversion with BioSQL taxon, and output as Embl OS/OC fields.

I'm in favour of having a bunch of static properties (perhaps forming
an enum) in the one place corresponding to each of these. That'd serve
the immediate purpose of removing the error-prone duplication of
checks, and we can get flash later if we want/need to. Shall I make it
so?


Cheers,
Len.