[Bioperl-l] Proposal: SemanticMapping and call for info on Gene Objects

[Ewan Birney]

> E.g. let's take a small part of SO and turn it into a lispy perl
> datastructure:
>
> [schema=>
>   [gene=>[[isa=>"seqfeature"],
>           [coding=>1],
>           [class=>"Bio::GeneI"]]],
>   [noncoding-gene=>[[isa=>"gene"],
>           [coding=>0],
>           [class=>"Bio::NcGeneI"]]],
>   [transcript=>[[isa=>"seqfeature"],
>                 [partof=>"gene"],
>                 [class=>"Bio::TranscriptI"]]],
> ]
>
> Ewan will hate this... but it would be nice to have as much of the
> implementation specified dynamically by a "language" such as the above. Or
> at least have it as an implementation option. If not, at least let's try
> and keep the OM to SO mapping clean.
>

I hate this less than I used to, but I *still* think having well defined
interfaces (which funky implementations can do what they like to implement
them and be endlessly flexible) is a Good Thing as it enforces a contract
between two pieces of code which may not have seen each other before.

(On-the-fly ontology synchronisation is I guess conceptually possible but
I'd like to see that before we went for it)


As long as - Chris - you like the Interfaces, I don't mind if you
implement your Lispy system - as a point to note though that if someone
wants to be terribly boring a implement a vanilla perl implementation of
the interface you shouldn't be so snotty as to consider it completely
defunct because you can't use lambda calculus across it ;)



And guys - remember - whoever codes it wins the argument!