[GMOD-devel] Re: [Open-bio-l] Schema for genes & features&mappingsto assemblies

[Matthew Pocock]

> I actually don't know how others view biosql, but generally whether you consider it being the supposed low-level implementation or rather an API specification does have some impact on the design. With the present, very generic, ontology/value design of biosql there is a problem in treating it as an API from an application level perspective: there are a thousand ways to implement semantics, but a particular application will have a hard time understanding all thousand ways. That is, an application tagged 'runs off biosql' is not guaranteed at all to actually run off any biosql-compliant instance, unless 'biosql-compliant' includes a certain defined ontology being adhered to. Defining that ontology may not be an easy task, and it could be a controversial one, too. But it's probably necessary in order to establish Biosql as an API for sequence database / feature browsers.
> 
> 	-hilmar

How much of the knowledge about how to interpret the ontology can be 
encoded within the ontology itself? We could populate the ontology 
tables with a 'starter pack' uppon which you can build if necisary. If 
we had a small number of abstract relationships and types that everyone 
could understand (like relation, sub-type, composed-from, part-of, 
instance-of, implies-that, transiative) and if we could take two 
relationships and link them by one of these well-known relationships 
then most stuff should be possible to deduce e.g. sub-type SUB-TYPE 
relation or saying that feature A is contained by feature B could be 
explained by an ontology expression describing mapping features to sets 
of intengers (or integer/strand pairs) and performing set-wise 
comparisons on them. If we do this sensibly, we should not need 
thousands of bespoke ontology relations together with bespoke adapter 
behavior. This should be discovered by following a very small number of 
'fundimental' relations (>2, but can you think of more than 10 that need 
independant deffinitions?).

Just musing.

Matthew