=Paper=
{{Paper
|id=Vol-2285/ICBO_2018_paper_24
|storemode=property
|title=eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools
|pdfUrl=https://ceur-ws.org/Vol-2285/ICBO_2018_paper_24.pdf
|volume=Vol-2285
|authors=Edison Ong,Yongqun He,Jie Zheng
|dblpUrl=https://dblp.org/rec/conf/icbo/OngH018
}}
==eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools==
https://ceur-ws.org/Vol-2285/ICBO_2018_paper_24.pdf
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 1
eXtensible ontology development (XOD) using
web-based Ontoanimal tools
Edison Ong, Yongqun He Jie Zheng
University of Michigan Medical School University of Pennsylvania
Ann Arbor, MI, USA Philadelphia, PA, USA
Abstract—The eXtensible ontology development (XOD) (XOD2) focuses on the alignment of imported terms from
strategy proposes four principles to support interoperable and external ontologies and newly added terms with the same
robust ontology development. These principles include ontology semantic framework. Ontology design patterns (ODP) usage
term reuse, semantic alignment, design pattern usage, and (XOD3) emphasizes new term generation and existing term
community extensibility. In this software demo, we show how editing based on ODPs. Community extensibility (XOD4)
Ontoanimal tools (e.g., Ontofox, Ontodog, Ontorat, and states that the ontology should be co-developed and applied to
Ontokiwi) can be used to support the implementation of these more use cases by more people in a broader community. These
XOD principles. The development of the Cell Line Ontology XOD principles significantly support ontology interoperability
(CLO) is used for the demonstration.
and robust ontology development [1].
Keywords—eXtensible ontology development; XOD; Ontofox; The collection of Ontoanimal tools is a suite of web-based
Ontodog; Ontorat; Ontokiwi; Cell Line Ontology; CLO tools that are primarily developed to support ontology
development, visualization, query and analysis. Among the
I. INTRODUCTION Ontoanimal tools are Ontofox [2], Ontodog [3], Ontorat [4],
Hundreds of ontologies have been developed to support and Ontokiwi/Ontobedia [5]. These web tools are widely used
biomedical research. Given the increasingly large number of in the biomedical ontology community, especially for those
biomedical ontologies developed, it is important to ensure that who have no or limited software programming skills.
newly developed ontologies are interoperable with existing
ontologies. However, this is a very challenging problem. Fig. 1 illustrates the pipeline for applyingthe XOD
principles and Ontoanimal tools to support extensible
To address the ontology interoperability issue, the ontology development. In this software demonstration, we will
“eXtensible Ontology Development” (XOD) strategy is a introduce the XOD principles and Ontoanimal tools, and
newly proposed strategy for ontology development [1]. This desmonstrate how these can be used to develop the Cell Line
strategy includes four principles. Ontology term reuse (XOD1) Ontology (CLO), a community-based ontology in the field of
emphasizes the reuse of terms from existing reliable ontologies cell lines and cell line cells [6].
instead of reinventing the wheel. Ontology semantic alignment
If terms exist in existing ontologies
XOD 1 XOD 3
If ODP ODP-based term
Reuse terms from
reliable ontologies
applicable generation
(Ontofox, Ontodog) (Ontorat)
New ontology
formation Add more terms
by term reuse & semantics
& alignment XOD 2
XOD 2
Align semantic If ODP Align & add term to
framework not ontology
(Ontofox, Ontobeep) applicable
XOD 4: Community extensibility (tools: Ontodog, Ontokiwi, Ontobedia)
Fig. 1. Pipeline of applying XOD principles and associated Ontoanimal tools for eXtensible ontology development.
[2] and Ontodog [3] can be used to support the extraction of
II. XOD PRINCIPLES SUPPORTED BY ONTOANIMAL TOOLS terms from other ontologies. Ontofox
A. Reuse terms (XOD1) using Ontofox and Ontodog (http://ontofox.hegroup.org/) extracts selected classes,
properties, annotations, and their related terms from source
Instead of reinventing the wheel, XOD 1 emphasizes the ontologies and saves the results in the OWL format [2].
reuse of terms from existing reliable ontologies. Both Ontofox Ontofox can extract different levels of intermediate terms
ICBO 2018 August 7-10, 2018 1
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 2
between the required terms and a chosen higher level or top D. Community extensibility (XOD4) using Ontodog and
term.The levels of intermediate terms to be extracted can be Ontokiwi
customized in Ontofox. Ontodog (http://ontodog.hegroup.org/) XOD 4 states that the ontology should be co-developed and
can also extract a subset of ontology terms and axioms. Unlike applied to more use cases by more people in a broader
Ontofox, Ontodog uses Excel or tab-delimited input files to community. Ontodog supports the generation of an ontology
identify which terms to retrieve and the users can also add community view, which can include community-specific
user-specified annotations to the retrieved terms. Both Ontofox annotations, such as ‘user-preferred label’, and be generated for
and Ontodog can generate OWL output files, which can be the complete ontology or a subset of it [3]. Ontokiwi is an
imported to a newly developed ontology. application that combines the features ofWikipedia-like
As an example of how XOD1 can be applied to new community discussion features and Ontobee-like semantical
ontology development, Ontofox was first used to extract ontology display and visualization features on the same
related terms from many existing ontologies such as the website [5]. As an Ontokiwi-based application, Ontobedia
Ontology for Biomedical Investigations (OBI), Cell Ontology (http://ontobedia.hegroup.org/) provides the users a platform
(CL), and UBERONmulti-species anatomy ontology. All the for importing, editing, annotating, and discussing structured
ontologies. In our software demonstration, we will show to the
Ontofox output OWL files were then imported to the CLO
attendees how we can edit the Ontobedia website for the
ontology using the owl:imports feature.
described features [5].
B. Semantic alignment (XOD2) using Ontofox and Ontobeep
III. SUMMARY AND DISCUSSION
XOD2 focuses on the alignment of imported terms from
existingontologies and newly added terms with the same The XOD principles provide a state-of-the-art strategy for
semantic framework. The top level ontology alignment can be efficient, effective, and extensible ontology development.
designed and conducted manually. It is suggested to reuse Ontoanimal tools provide a good suite of tools to support the
terms from ontologies (e.g., OBO ontologies) that follow the XOD-based ontology development. The CLO development use
same semantic structure. Ontofox supports semantic alignment casedemonstrates how such XOD strategy can be achieved
by automatically extracting semantic axioms [2]. With this with the Ontoanimal tools.
feature, all the OWL files of OBO ontologies imported to CLO In addition to the web-based Ontoanimal tools, many other
were well aligned. In cases where Ontofox-assigned alignment tools, such as the web-based WebProtege tool
did not align well, manual checking and alignment need to be (https://webprotege.stanford.edu/) and the command-line tool
used. For the manual status checking, Ontobeep ROBOT (https://github.com/ontodev/robot), are available to
(http://www.ontobee.org/ontobeep) can be used to compare support XOD principles, and are summarized in the original
two or three ontologies, e.g., CLO, OBI, and CL, and identify XOD paper [1].
whether these different ontologies are aligned with the same
semantic framework. ACKNOWLEDGMENT
C. ODP-based term generation (XOD3) using Ontorat The development of Ontoanimal tools was primarily
Instead of adding one new term or editing one existing term supported by a NIH R01 grant (1R01AI081062). The CLO and
at a time, XOD 3 emphasizes the addition or editing of a group LINCS work were supported by an external data science
of terms based on ontology design patterns (ODPs). Ontorat research award of the grant U54HL127624 (BD2K LINCS
(http://ontorat.hegroup.org) generates and edits ontology terms Data Coordination and Integration Center, DCIC).
and axioms and provides term annotations [4]. Ontorat uses REFERENCES
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