<div>Greetings,</div>
<div>Am in Australia - can keep in touch. Jim and I are continuing to work in this area...</div>
<div> </div>
<div>P.</div>
<div><br><br> </div>
<div class="gmail_quote">On Wed, Nov 4, 2009 at 5:03 PM, Jim Downing <span dir="ltr"><<a href="mailto:ojd20@cam.ac.uk">ojd20@cam.ac.uk</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Carl, all,<br><br>We've been looking through the ontology and had a few comments.<br>Apologies if these have been asked and dealt with before now, I'm only<br>
just getting up to speed with the ontological modeling.<br><br>* The "referencesExperiment" and "referencesMolecularEntity"<br>predicates seem misplaced. If these are references, shouldn't they be<br>
subPropertyOf references, rather than aggregates? We probably need<br>both - we might want to link to an entry on PubChem for a molecule and<br>/ or to a data file that is part of the enhanced publication.<br><br>* Should / could we use chemaxiomChemDomain:MolecularEntity as the<br>
range of the molecular entity properties?<br><br>* There's something screwy going on with the dcterms in protege - they<br>seem to be sub-classes of themselves - any idea what's going on?<br><br>* The hasDataRepresentation/hasFigure, hasTable, hasDataSet seems<br>
either too detailed or too brief - if tables, why not sections,<br>appendices etc, which will be also be useful for our analysis?<br><br>In my mind this is related to the issue of whether we include<br>"aboutness" semantics - I think we need to if we want to represent a<br>
full provenance chain for the distributed process (which would be very<br>cool to do). I'd imagined something like: -<br><br>psu:publication1 orechem:hasComponent psu:<a href="http://narrative1.ps/" target="_blank">narrative1.ps</a> .<br>
psu:<a href="http://narrative1.ps/" target="_blank">narrative1.ps</a> orechem:hasComponent soton:experimentalSection1 .<br>soton:experimentalSection1 orechem:about cam:moleculeX .<br>cam:moleculeX a chemaxiom:MolecularEntity ; orechem:referenceMolecule<br>
crystaleye:actae/foo/bar/234 .<br>iu:gauin1 a chemaxiom:ComputationalInput; orechem:derivedFrom cam:moleculeX .<br>iu:gauout1 orechem:derivedFrom iu:gauin1.<br><br>To do this I get the impression we need to use classes from chemaxiom,<br>
and to define some more of our own.<br><br>* In a sense we are generating multiple, incrementally enhanced<br>manifestations of the same work. Bibo doesn't seem to have the power<br>to describe the FRBR notions of Work, Manifestation and Representation<br>
as separate, related abstractions. Do we need to?<br><br>More tomorrow after more analysis!<br><br>Best regards,<br>jim<br><br>_______________________________________________<br>Orechem mailing list<br><a href="mailto:Orechem@openarchives.org">Orechem@openarchives.org</a><br>
<a href="http://www.openarchives.org/mailman/listinfo/orechem" target="_blank">http://www.openarchives.org/mailman/listinfo/orechem</a><br></blockquote></div><br><br clear="all"><br>-- <br>Peter Murray-Rust<br>Reader in Molecular Informatics<br>
Unilever Centre, Dep. Of Chemistry<br>University of Cambridge<br>CB2 1EW, UK<br>+44-1223-763069<br>