[MOBY-l] Biomoby and Taverna 1.2

[markw at illuminae.com]

Quoting Tom Oinn <tmo at ebi.ac.uk>:

> - if the set of sequences becomes some opaque type without this
> information then you can't do this. 

Nothing becomes opaque by putting it in the MOBY data-typing system - it can
only get richer and more meaningful by assigning it a specific class :-) 
Generic services that operate on lower ontological classes will still be
discovered and executed, so this use case still fails the test of need.


> Strikes me that you need a more
> sophisticated typing scheme to do this, perhaps extending the Collection
> concept to allow the imposition of semantics to the group of child
> objects?

Creating a new type of element - limitedCollection or something like that -
would be an alternative... or changing the definition of Collection to "zero or
more" rather than "one or moe" would also allow us to terminate the recursion.


> I think you do need nested collections though, it's not
> impossible to deal with (we have some slightly twisted code in Taverna
> to do it but it works well enough)

Probably we do... but I find it hard to believe that we will have sets of sets
of sets of sets where there is no implicit semantic meaning at any level!  As
soon as there is semantic meaning, it should be a fully qualified MOBY Object
rather than an arbitrary collection.... IMO :-)

M



> 
> Tom
>