It's not a protocol in my book - Deepak Singh from iPhone

False choice. Calling it a "service" might be more fitting (it has both a protocol and a data format). - Shiran Pasternak

Shiran, then you would say DAS (service) = HTTP/SOAP (protocol) + XML (format)? - Andrew Su

That's pretty much what all web services are aren't they? REST/SOAP + XML/JSON - Deepak Singh

DAS is a layer on top of these standards. The protocol describes how a client defines object types (e.g., genes) and coordinate slices; The data format describes how the results are represented in XML. - Shiran Pasternak

@Shiron does DAS really defines what is the type of object ? I mean, is "gene" a simple word or is it a component of an ontology ? - Pierre Lindenbaum

@Pierre DAS only defines "feature" as a type. There is no sequence ontology (not last time I looked). But it's up to the provider to define the interface so that a client can request meaningful objects like "genes" (or "pierres," for all it cares). - Shiran Pasternak

thanks - Pierre Lindenbaum

thanks all for the comments. Personally I think this is largely semantics, but I suppose if we talk about it in a paper the semantics should be right... - Andrew Su

There is a sequence ontology http://is.gd/58anp And many of the Gene Ontology folks seem to be associated with it. But I don't think it has really taken off it terms of use. Still feeling it out. - Andrew Warren