=Paper=
{{Paper
|id=Vol-2931/ICBO_2019_paper_44
|storemode=property
|title=Where Does an Ontology Start?
|pdfUrl=https://ceur-ws.org/Vol-2931/ICBO_2019_paper_44.pdf
|volume=Vol-2931
|authors=Henriette Harmse,Melanie Courtot,Warren Read,Nico Matentzoglu,David Osumi-Sutherland,Simon Jupp
|dblpUrl=https://dblp.org/rec/conf/icbo/HarmseCRMOJ19
}}
==Where Does an Ontology Start?==
https://ceur-ws.org/Vol-2931/ICBO_2019_paper_44.pdf
Where does an Ontology start?
Henriette Harmsea, Melanie Courtota, Warren Reada, Nico Matentzoglua, David Osumi-
Sutherlanda, Simon Juppa
a
The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Abstract
A good ontology design practice is to define terms based on Implementation
terms from upper ontologies. Hence, the terms of the current
ontology often are found deep down the hierarchy, which OLS has been extended support the use of a new OWL
users can find confusing. Here we suggest ways to deal with annotation property with the IRI
this. http://www.ebi.ac.uk/ols/vocabulary/hasPreferredRootTerm which
can be used on the ontology to assert the set of class IRIs that
Keywords:
can be considered as roots. OLS will detect this property and
visualisation, tree, roots change how the class hierarchy is rendered by default to only
show the root terms, as specified by the property. The full
Introduction classification is preserved internally, and users are able to
easily switch (via radio button selection) to see the fully
Biomedical ontologies have become important in the expanded classification if they wish.
biological and medical domains through their provisioning of
common controlled vocabularies. A model of good practice Discussion
guiding the design of biomedical ontologies is to define terms
based on terms from common higher level ontologies (1). In The interest and use of ontologies continues to increase in the
the OBO community the use of upper-level ontologies, such as life sciences, but we need to be able to effectively present and
BFO (1), is recommended. While upper-ontologies bring value communicate these ontologies to a wide audience of users. In
for the interoperability of ontologies, they often contain terms some cases this means hiding the complexity of the underlying
that are hard to understand for non-ontologists (2). Yet these machinery, such as OWL or upper-level ontologies. With over
terms are often the first thing a user is presented with when 65 ontologies in OLS alone that start with a root concept of
exploring an ontology, especially if the ontology class “Entity”, our simple proposal could significantly improve the
hierarchy is being presented using a standard tree-based way these ontologies are presented to users.
visualisation. We are exploring additional ways to simplify the presentation
To alleviate this, we propose a standard annotation property to of root terms that include detecting root terms based on OBO
indicate to visualisation tools what is the set of classes that namespaces of the presence of terms in the OBO Core1. There
should be considered root concepts of the ontology. Online may also be other more appropriate vocabularies for
ontology browsers and visualisation tools can use this expressing this information within an ontology, such as the use
information to render the ontology and highlight where the of SKOS concept schemes. At this stage we are open to
root concepts sit in the hierarchy. To illustrate the issues we working with the community to collect more use-cases and
present an example from the Data Use Ontology (DUO) and welcome feedback on the approach presented here.
support for a new “hasPreferredRootTerm” annotation
property for ontologies hosted by the EMBL-EBI Ontology
References
Lookup Service (OLS).
The DUO provides standard codes to indicate the secondary
1. Smith B, Ashburner M, Rosse C, Bard J, Bug W,
use restrictions and conditions on scientific data sharing. It
Ceusters W, et al. The OBO Foundry: Coordinated Evolution
imports a number of ontologies which are used as the basis on
of Ontologies to support Biomedical Data Integration. Nature
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biotechnology. 2007;25(11):1251-5.
and BioPortal, and both browsers present the DUO root
2. Stevens R, Lord P, Malone J, and Matentzoglu N.
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Measuring Expert Performance at Manually Classifying
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Domain Entities under Upper Ontology Classes: 2018;
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as these are buried six levels deep in the hierarchy under the
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1
https://github.com/OBOFoundry/Experimental-OBO-Core
Copyright © 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).