The question is how MP and DIDEO work together. I think that the main thing is to always remember the distinction between the evidence base and the knowledge base. To generate a PDDI knowledge base, we do not do inference over the entire evidence base. Rather, just those NP:Assertions that formalize MP:Claims with MP:Data with an MP:Method meeting some belief criteria.
With this in mind, there are three points of DIDEO integration.
One is with the entities represented as OWL RDF in NP:Assertion instances. The use of DIDEO for this is very direct because the NP:Assertions are written in OWL using DIDEO and the resulting RDF is inserted into the evidence base.
Another, is to assign at type to MP:Method instances.The use of DIDEO for the latter is being implemented (e.g., see this draft). The idea is currently that RDF created using MP:Data and MP:Methods will be sent to an OWL DL reasoner to infer the exact evidence type according to DIDEO. This will then be stored in the MP graph such that it is clear that it either is an MP:Method instance, or is the DIDEO evidence type of an MP:Method instance. @jodischneider - can MP:Methods be MP:formalizedAs the same way that MP:Claims are? Maybe that would be a good solution so that we don’t break things from an ontology perspective
Finally, the data attached to MP:Data will need to be represented in a logically consistent manner that is concordant with OBI practices. We have worked through several different data examples such as drug Clearance. I think the trick here is to create the instance representation under an MP:Data instance, but using OBI and DIDEO properties. We can probably discuss departing from the idea of using DIKB specific Data and Material instances which seemed important previously but shouldn’t be necessary so long as the MP:Method connects to a DIDEO evidence type which can be used by client programs to know what exact data and method resources.