[Orechem] Ontology comments

[Jim Downing]

Hi Carl, all,

We've been looking through the ontology and had a few comments.
Apologies if these have been asked and dealt with before now, I'm only
just getting up to speed with the ontological modeling.

* The "referencesExperiment" and "referencesMolecularEntity"
predicates seem misplaced. If these are references, shouldn't they be
subPropertyOf references, rather than aggregates? We probably need
both - we might want to link to an entry on PubChem for a molecule and
/ or to a data file that is part of the enhanced publication.

* Should / could we use chemaxiomChemDomain:MolecularEntity as the
range of the molecular entity properties?

* There's something screwy going on with the dcterms in protege - they
seem to be sub-classes of themselves - any idea what's going on?

* The hasDataRepresentation/hasFigure, hasTable, hasDataSet seems
either too detailed or too brief - if tables, why not sections,
appendices etc, which will be also be useful for our analysis?

In my mind this is related to the issue of whether we include
"aboutness" semantics - I think we need to if we want to represent a
full provenance chain for the distributed process (which would be very
cool to do). I'd imagined something like: -

psu:publication1 orechem:hasComponent psu:narrative1.ps .
psu:narrative1.ps orechem:hasComponent soton:experimentalSection1 .
soton:experimentalSection1 orechem:about cam:moleculeX .
cam:moleculeX a chemaxiom:MolecularEntity ; orechem:referenceMolecule
crystaleye:actae/foo/bar/234 .
iu:gauin1 a chemaxiom:ComputationalInput; orechem:derivedFrom cam:moleculeX .
iu:gauout1 orechem:derivedFrom iu:gauin1.

To do this I get the impression we need to use classes from chemaxiom,
and to define some more of our own.

* In a sense we are generating multiple, incrementally enhanced
manifestations of the same work. Bibo doesn't seem to have the power
to describe the FRBR notions of Work, Manifestation and Representation
as separate, related abstractions. Do we need to?

More tomorrow after more analysis!

Best regards,
jim