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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 8th
of May, 9am
End 8th
of May, 4pm
Requirement Participants
will need their own laptop with the software listed below installed before the
workshop.
Registration email to p.grobe@leibniz-zfmk.de
or to lars.m.vogt@googlemail.com; no registration fee applies
Reference to a follow-on workshop On 9th to 10th of May, a workshop on "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.
Building 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