[Orechem] Ontology comments

[Peter Murray-Rust]

Greetings,
Am in Australia - can keep in touch. Jim and I are continuing to work in
this area...

P.



On Wed, Nov 4, 2009 at 5:03 PM, Jim Downing <ojd20 at cam.ac.uk> wrote:

> 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
>
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-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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