<span id="internal-source-marker_0.34961665142327547"><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline"><font face="'Times New Roman'" size="3"><span style="white-space:pre-wrap">Following is a workshop of broad interest to many of you. If you are interested in attending or have further questions, please contact John Deck (<a href="mailto:jdeck@berkeley.edu">jdeck@berkeley.edu</a>). Note that there is a limited time in which to make your guaranteed hotel reservations at the The Oread hotel in Lawrence, under the "Biodiversity Semantics Workshop", which must be done before April 15th to get the reserved rate.</span></font></span></p>
<p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3"><br></font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt">
<span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3">Feel free to forward or post.</font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt">
<span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3"><br></font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3">Cheers,</font></span></p>
<p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3">John</font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt">
<span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3">*******</font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3"><br>
</font></span></p><p dir="ltr" style="text-align:left;margin-top:0pt;margin-bottom:0pt"><span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3">Google Doc link describing workshop and agenda:</font></span></p>
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<span style="vertical-align:baseline;white-space:pre-wrap"><font face="'Times New Roman'" size="3"><a href="https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9L0Vk/edit">https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9L0Vk/edit</a></font></span></p>
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<font face="'Times New Roman'" size="3"><span style="white-space:pre-wrap">Text Description of above google doc link:</span></font></p><p dir="ltr" style="font-weight:bold;font-family:Times;font-size:medium;text-align:center;margin-top:0pt;margin-bottom:0pt">
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<span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Semantics of Biodiversity Workshop May 16 - 18, 2012</span></p><p dir="ltr" style="font-weight:bold;font-family:Times;font-size:medium;text-align:center;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">University of Kansas Biodiversity Institute</span><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap"> -- </span><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Lawrence, Kansas</span></p>
<p dir="ltr" style="font-weight:bold;font-family:Times;font-size:medium;text-align:center;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Times New Roman';font-style:italic;vertical-align:baseline;white-space:pre-wrap">Sponsored by RCN4GSC, Morphbank, Kansas University Biodiversity Informatics Center, </span></p>
<p dir="ltr" style="font-weight:bold;font-family:Times;font-size:medium;text-align:center;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Times New Roman';font-style:italic;vertical-align:baseline;white-space:pre-wrap">and BiSciCol in collaboration with the National Center for Biomedical Ontology</span></p>
<b><span style="font-family:'Times New Roman';font-style:italic;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br><span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">ABOUT THE SPEAKER</span><br>
<b><span style="font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br><span style="font-size:15px;font-family:'Times New Roman';color:rgb(51,51,51);font-weight:normal;vertical-align:baseline;white-space:pre-wrap">Barry Smith is a prominent contributor to ontology research in biomedical and other domains. He is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, a PI on the Protein Ontology and Infectious Disease Ontology projects, and one of the founders of the Open Biomedical Ontologies (OBO) Foundry initiative.</span><br>
<span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">TOPICS</span><br>
<b><span style="font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">The Semantics of Biodiversity Workshop will explore terms used to describe biological collection objects and their derivatives using the Darwin Core standard as a starting point. The goal is to enable linking data across domains and to produce a deeper understanding of our planet’s biodiversity. For example, by linking information about the ecosystem (both gross and micro-habitat) and the geospatial environment to tissue samples and derived sequences, we can better understand population dynamics, ecosystem gene expression, and the significance of biodiversity in different environments.</span><br>
<span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">While the biodiversity informatics community has made much progress in standardizing terms over the last 20 years, specific problem areas are encountered both within and between relevant standards domains. Drawing on community discussions from the TDWG and GSC communities, and using the experiences of OBO in integrating information, Smith will guide a discussion of term clarification for the Darwin Core standard. Some example discussion topics are:</span><br>
<span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">How do samples and occurrences relate to each other?</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">How can we best distinguish between collection objects, observations, and individuals?</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">What is the nature of the relationship between habitats, environments, and environmental materials?</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">What is the difference between a set, a lot, and a collection?</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">How to deal with taxonomic names associated with collection objects? </span></li>
</ul><span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">Much of the workshop will be devoted to these and other discussion topics that will be introduced by attendees. Come prepared with your topics and/or important darwin core terms and be able to introduce them. It will be helpful to indicate before the workshop what topic you can introduce at the meeting by emailing </span><a href="mailto:jdeck@berkeley.edu" style="font-weight:bold;font-family:Times;font-size:medium"><span style="font-size:15px;font-family:'Times New Roman';color:rgb(17,85,204);font-weight:normal;vertical-align:baseline;white-space:pre-wrap">jdeck@berkeley.edu</span></a><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">. </span><b><span style="font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br>
<b><span style="font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br><span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Day 1 (Wednesday, May 16th)</span><br>
<span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">9am - 5:30pm </span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">Coffee & treats Wednesday and Thursday hosted by KU</span><br>
<span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">Breakfast at Hotel all 3 days</span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">Lunch and dinner on your own, with plenty of options within walking distance</span><br>
<span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap">Background and problem statement (Wednesday)</span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Review successful examples from other communities </span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Getting clear on the distinctions between objects, data, and metadata</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Contrasting annotation with metadata</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Relationship expressions. </span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Tracking Identifiers to refer to objects or classes uniquely. </span></li>
</ul><span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap">Applying ontological principles to our subject domain (Wednesday and Thursday)</span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Interactive review of 10 or so of the most important Darwin core terms from the ground up. Participants will be describing terms and the intention behind their original formation. Come prepared to discuss your term(s) of interest.</span></li>
</ul><span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap">6pm- 7:30pm Reception hosted by Kansas University’s Biodiversity Institute</span><br>
<span style="font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Day 2 (Thursday, May 17th)</span><br>
<span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">9am - 5:30pm </span><br><span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br>
<span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap">Solutions for the future (Thursday)</span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline"><span style="font-size:15px;vertical-align:baseline;white-space:pre-wrap">Enabling linked data </span></li>
<li style="list-style-type:disc;font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline"><span style="font-size:15px;vertical-align:baseline;white-space:pre-wrap">Pitfalls, traps, and planning</span></li>
<li style="list-style-type:disc;font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline"><span style="font-size:15px;vertical-align:baseline;white-space:pre-wrap">Creating a sociology so people can re-use ontologies</span></li>
</ul><span style="font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;font-style:italic;vertical-align:baseline;white-space:pre-wrap">Planning the 3rd Day discussions (4-5:30pm on Thursday)</span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline"><span style="font-size:15px;vertical-align:baseline;white-space:pre-wrap">Barry will be departing at 4pm on Thursday and so we will use the remainder of day to plan our discussion for Friday.</span></li>
</ul><b><span style="font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap;font-size:15px;font-size:15px"></span></b><br><span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Day 3 (Friday, May 19th)</span><br>
<span style="font-weight:bold;font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">9am - Noon</span><br><span style="font-size:15px;font-family:'Times New Roman';font-weight:normal;vertical-align:baseline;white-space:pre-wrap">We will be collecting discussion topics on Thursday afternoon for our Friday discussion. Some possible topics include:</span><ul style="font-weight:bold;font-family:Times;font-size:medium;margin-top:0pt;margin-bottom:0pt">
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Develop concrete proposals for Darwin Core term clarification</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Do we need a new namespace for Darwin Core (for enforcing URIs)?</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Implications for MIxS Standard</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Implications for the Darwin Core Archive Format</span></li>
<li style="list-style-type:disc;font-size:13px;font-family:symbol;font-weight:normal;vertical-align:baseline"><span style="font-size:15px;font-family:'Times New Roman';vertical-align:baseline;white-space:pre-wrap">Recommendations to the TDWG-RDF Group</span></li>
</ul></span><div><br></div>-- <br>John Deck<br>(541) 321-0689<br><br>