[tdwg] Reminder for Workshop “An Introduction to Anatomy Ontologies”, ZFMK Bonn, 8th May 2019

Lars Vogt lars.vogt at zoosyst-berlin.de
Thu Apr 18 13:48:52 UTC 2019


**We still have a few places available for our workshop “An Introduction 
to Anatomy Ontologies”, ZFMK Bonn, 8th May 2019.


Join us for one day and get an introduction to the creation of anatomy 
ontologies.*
*


*An Introduction to Anatomy Ontologies*

*Synopsis*
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.

*Logistics**
Venue*Zoological Research Museum Alexander Koenig (ZFMK), Seminarraum 
(seminar room), Adenauerallee 160, 53113 Bonn, Germany*
Start*8^th of May, 9am*
End*8^th of May, 4pm*
Requirement*Participants will need their own laptop with the software 
listed below /installed before the workshop/.*
Registration*email to p.grobe at leibniz-zfmk.de or to 
lars.m.vogt at googlemail.com;no registration fee applies

*Reference to a follow-on workshop*On 9^th to 10^th of May, a workshop 
on "Semantic Data Models in Anatomy 
<https://www.zfmk.de/de/forschung/tagungen-und-konferenzen/workshop-semantic-data-models-in-anatomy>" 
will be held at the same venue.


*Target Audience*
Researchers, or upper-level undergraduate to graduates whose research 
contains some component of morphology.No technical (computer/software) 
knowledge is required, though note that using ontologies is a technical 
exercise. Our overview will be conceptual rather than a deep dive.


*Syllabus*
*What is an Ontology? (what)*
What is/not an ontology? Should you use ontologies?Why/not?Basic 
concepts: classes, instances, relationships (object properties), 
orthogonality, true-path, labels, URIs. Ontology formats, languages and 
syntaxes.

*Anatomy and ontologies (why)*
How ontologies are currently being used in current morphological 
research.Benefits. Design considerations: hierarchies and 
granularity.Best practices- definitions, reuse. Taking small steps: many 
vs. few relationships.

*B**uilding and Curating ontologies - Software and Tools (how)*
Building ontologies piecemeal, or extracting them automatically.Author 
driven vs annotator based ontologies. Ontology editors (OBO Edit. 
Protégé. Mx. Web-Protégé). An example ontology: skeletomuscular system 
of the insect thorax.

*Formalizing morphology descriptions: from simple annotation to formal 
descriptions - (why and how)*
Concepts for re-use and integration with tools such as Onto-fox and 
Noctua. Class based vs instance based formal descriptions. Manchester 
syntax.

*Using ontologies as knowledge bases (when)*
HAO, OaRCS. Flybase. Phenoscape. Quantitative analyses.

*Community resources (who)*
Listservs, tools, meetings. Other ontology courses, tutorials. Other 
experts creating and modifying ontologies. Next steps.


**Software**
Please have the following software install and/or visit websites prior 
to the workshop

  * Protégé - https://protegewiki.stanford.edu/wiki/Install_Protege5
  * OARCS -
    http://oarcs.speciesfilegroup.org/projects/99/public/ontology_class/show_expanded/10203
  * HAO - http://portal.hymao.org/projects/32/public/ontology/



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