Hi Roger,<div><br></div><div>I was wondering if you needed any help?</div><div><br></div><div>I have using Protege. And most recently I have been trying to make my ontology work with the other major ontologies and TDWG.</div>
<div><br></div><div>The items that I needed, that were not there originally, were a SpeciesConceptID (different from the name) and the ability to play well with the LinkedData community.</div><div><br></div><div>These two issues seem to have been resolved. :-)</div>
<div><br></div><div>- Pete</div><div><br></div><div>Also, Protege is free <a href="http://protege.stanford.edu/">http://protege.stanford.edu/</a><br><br><div class="gmail_quote">On Tue, May 12, 2009 at 3:59 AM, Roger Hyam <span dir="ltr"><<a href="mailto:rogerhyam@mac.com">rogerhyam@mac.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">Hi All,<div><br></div><div>I need to do some work on the Taxon Name and Taxon Concept vocabularies and believe I have come up with a good way of organising the TDWG ontology space (everything within http:/<a href="http://rs.tdwg.org/ontology" target="_blank">rs.tdwg.org/ontology</a>).</div>
<div><br></div><div>The following are the changes I suggest:</div><div><br></div><div><ul><li>All files should be OWL DL compliant </li><li>All files should be openable in Protege 4 (I believe this is now good enough to use for editing these small ontologies)</li>
<li>We take a highly structured modular approach I call this the Bricks and Mortar design pattern</li><ul><li>Some files are 'Bricks' and as such <b>import or reference no other files, classes or individuals</b>. e.g. TaxonName does not mention a higher 'Name' object in the class hierarchy.</li>
<li>Other files are 'Mortar'. These files import Bricks and stipulate relationships between things. Because we are using OWL it is easy to define things like the class hierarchy or the range of a property in a separate file to the file the original class or property was defined in.</li>
<li>This pattern gives us maximum re-usability as the same Brick could be used in different ways. It does not bind us to any one implementation of one object.</li><li>An example of the usage pattern would be to define TaxonName, TaxonConcept, Rank, NomenclaturalCode as separate bricks that don't reference each other at all then create a TCS ontology that imports these 4 bricks and defines their relationships.</li>
</ul><li>We move to some other method of presenting the ontologies on line - possibly the OWLDoc plug-in for Protege. This would lose us the branded look we have at the moment but would be more flexible and consistent in the long run.</li>
</ul><div><br></div><div>As I need to do this for the TaxonName TaxonConcept vocabularies I volunteer to do manage the space this year if people are happy going down this route.</div><div><br></div><div>From the point of view of deployed systems (the nomenclators) there may be a need for a namespace change on some properties but I would review what is in use and this would be trivial - if necessary at all.</div>
<div><br></div><div>What do you think? I will take silence as acquiescence on the grounds that any movement is better than none - though I don't suppose I will get round to doing anything about changes till after e-Biosphere in June.</div>
<div><br></div><div>All the best,</div><div><br></div><div>Roger</div><div><br></div></div><div><div> <span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word">
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<div><br>-----------------------------------------------------</div><div> Roger Hyam - Project Officer WP4</div><div> Pan European Species Infrastructure</div><div> +44 75 90 60 80 16</div><div>-----------------------------------------------------</div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>---------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>
1630 Linden Drive<br>Madison, WI 53706<br>------------------------------------------------------------<br>
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