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<p class="MsoTitle" style="mso-outline-level:1"><font size="+3"><b><span
style="font-size:16.0pt;font-family:"FreeSans","sans-serif""
lang="EN"><font size="+2">An Introduction to Anatomy
Ontologies</font></span></b></font></p>
<p class="MsoTitle" style="mso-outline-level:1"><font size="+3"><b><span
style="font-size:16.0pt;font-family:"FreeSans","sans-serif""
lang="EN"><font size="+2"><font size="+1">Synopsis</font></font></span></b></font><span
lang="EN"><br>
This workshop is a brief introduction for researchers that are
interested in formalizing how they formally represent the
anatomy they study. Around half the content will cover what
ontologies are, and how they can be used, the other half will
focus on what concerns and issues arise when referencing anatomy
in ontologies. The focus will be on existing ontologies and
tools rather than future theoretical avenues, though resources
of this type will be mentioned. The skeletomuscular system of
arthropods will be used as an example. The workshop will be
interactive, though most interactions will be discussion-based
rather than tool based tutorials, this is a reflection of the
available time. An honest, experienced appraisal of the pros-and
cons of using ontologies for morphological research will be the
cornerstone for discussion and questions. The workshop will be
lead by Drs. István Mikó and Matt Yoder.</span> </p>
<p class="Heading1" style="mso-outline-level:1"><b><span
style="font-size:14.0pt" lang="EN">Logistics</span></b><b
style="mso-bidi-font-weight:normal"><span lang="EN"><br>
<font size="-1">Venue</font></span></b><span lang="EN"><font
size="-1"><span style="mso-spacerun:yes"> </span><span
style="mso-tab-count: 1"> </span>Zoological
Research Museum Alexander Koenig (ZFMK), Seminarraum (seminar
room), Adenauerallee 160, 53113 Bonn, Germany</font></span><b
style="mso-bidi-font-weight:normal"><span lang="EN"><br>
<font size="-1">Start</font></span></b><span lang="EN"><font
size="-1"><span style="mso-spacerun:yes"> </span><span
style="mso-tab-count:1"> </span>8<sup>th</sup>
of May, 9am</font></span><b
style="mso-bidi-font-weight:normal"><span lang="EN"><br>
<font size="-1">End</font></span></b><span lang="EN"><font
size="-1"><span style="mso-spacerun:yes"> </span><span
style="mso-tab-count:1"> </span>8<sup>th</sup>
of May, 4pm</font></span><b
style="mso-bidi-font-weight:normal"><span lang="EN"><br>
<font size="-1">Requirement</font></span></b><span lang="EN"><font
size="-1"> <span style="mso-tab-count:1"> </span>Participants
will need their own laptop with the software listed below <i
style="mso-bidi-font-style: normal">installed before the
workshop</i>.<span style="mso-spacerun:yes"></span></font></span><b
style="mso-bidi-font-weight:normal"><span lang="EN"><br>
<font size="-1">Registration</font></span></b><span lang="EN"><font
size="-1"><span style="mso-spacerun:yes"> </span><span
style="mso-tab-count: 1"> </span>email to <a
class="moz-txt-link-abbreviated"
href="mailto:p.grobe@leibniz-zfmk.de" moz-do-not-send="true">p.grobe@leibniz-zfmk.de</a>
or to <a class="moz-txt-link-abbreviated"
href="mailto:lars.m.vogt@googlemail.com"
moz-do-not-send="true">lars.m.vogt@googlemail.com</a>;</font></span><font
size="-1"><span lang="EN"> no registration fee applies</span></font>
<br>
<span style="font-size:14.0pt" lang="EN"></span></p>
<p> </p>
<p class="MsoNormal" style="margin-left:85.5pt;text-indent:-85.5pt"><span
lang="EN"></span><font size="-1"><b
style="mso-bidi-font-weight:normal"><span lang="EN">Reference
to a follow-on workshop</span></b></font><span lang="EN"><span
style="mso-spacerun:yes"> </span><font size="-1">On 9<sup>th</sup>
to 10<sup>th</sup> of May, a workshop on "<a
moz-do-not-send="true"
href="https://www.zfmk.de/de/forschung/tagungen-und-konferenzen/workshop-semantic-data-models-in-anatomy">Semantic
Data Models in Anatomy</a>" will be held at the same venue.</font></span></p>
<p class="MsoNormal"><span lang="EN"><span style="mso-spacerun:yes"> </span></span><br>
<span lang="EN"><span style="mso-spacerun:yes"><b><span
style="font-size:14.0pt" lang="EN">Target Audience</span></b></span><br>
Researchers, or upper-level undergraduate to graduates whose
research contains some component of morphology.<span
style="mso-spacerun:yes"> </span>No technical
(computer/software) knowledge is required, though note that
using ontologies is a technical exercise. <span
style="mso-spacerun:yes"> </span>Our overview will be
conceptual rather than a deep dive.<span
style="mso-spacerun:yes"> <br>
</span></span></p>
<p class="MsoNormal"><span lang="EN"><span style="mso-spacerun:yes"><br>
</span></span></p>
<p class="Heading3" style="mso-outline-level:1"><b><span
style="font-size:14.0pt" lang="EN">Syllabus</span></b><br>
<b><span lang="EN">What is an Ontology? (what)</span></b><span
lang="EN"><br>
What is/not an ontology? Should you use ontologies?<span
style="mso-spacerun:yes"> </span>Why/not?<span
style="mso-spacerun:yes"> </span>Basic concepts: classes,
instances, relationships (object properties), orthogonality,
true-path, labels, URIs. Ontology formats, languages and
syntaxes. </span> </p>
<p class="MsoNormal"><span lang="EN"><b>Anatomy and ontologies (why)</b><br>
How ontologies are currently being used in current morphological
research.<span style="mso-spacerun:yes"> </span>Benefits.
Design considerations: hierarchies and granularity.<span
style="mso-spacerun:yes"> </span>Best practices-
definitions, reuse. Taking small steps: many vs. few
relationships.</span></p>
<p class="MsoNormal"><span lang="EN"><b>B</b><b>uilding and Curating
ontologies - Software and Tools (how)</b><br>
Building ontologies piecemeal, or extracting them automatically.<span
style="mso-spacerun:yes"> </span>Author driven vs annotator
based ontologies. Ontology editors (OBO Edit. Protégé. Mx.
Web-Protégé). An example ontology: skeletomuscular system of the
insect thorax.</span></p>
<p class="MsoNormal"><span lang="EN"><b>Formalizing morphology
descriptions: from simple annotation to formal descriptions -
(why and how)</b><br>
Concepts for re-use and integration with tools such as Onto-fox
and Noctua. Class based vs instance based formal descriptions.
Manchester syntax.</span></p>
<p class="MsoNormal"><span lang="EN"><b>Using ontologies as
knowledge bases (when)</b><br>
HAO, OaRCS. Flybase. Phenoscape. Quantitative analyses. </span></p>
<p class="MsoNormal"><span lang="EN"><b>Community resources (who)</b><br>
Listservs, tools, meetings. Other ontology courses, tutorials.
Other experts creating and modifying ontologies. Next steps.</span></p>
<p class="MsoNormal"><span lang="EN"><br>
</span></p>
<p class="MsoNormal" style="mso-outline-level:1"><span lang="EN"><b><b><span
style="font-size:14.0pt" lang="EN">Software</span></b></b><br>
Please have the following software install and/or visit websites
prior to the workshop</span><span lang="EN"><br>
</span></p>
<ul>
<li><span lang="EN">Protégé - <a
href="https://protegewiki.stanford.edu/wiki/Install_Protege5"
moz-do-not-send="true"><span class="InternetLink"><span
style="color:#1155CC">https://protegewiki.stanford.edu/wiki/Install_Protege5</span></span></a></span><span
lang="EN"></span></li>
<li><span lang="EN">OARCS - <a
href="http://oarcs.speciesfilegroup.org/projects/99/public/ontology_class/show_expanded/10203"
moz-do-not-send="true"><span class="InternetLink"><span
style="color:#1155CC">http://oarcs.speciesfilegroup.org/projects/99/public/ontology_class/show_expanded/10203</span></span></a></span><span
lang="EN"></span></li>
<li><span lang="EN">HAO - <a
href="http://portal.hymao.org/projects/32/public/ontology/"
moz-do-not-send="true"><span class="InternetLink"><span
style="color:#1155CC">http://portal.hymao.org/projects/32/public/ontology/</span></span></a></span></li>
</ul>
<p class="MsoNormal" style="mso-outline-level:1"> </p>
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