5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

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14 Citations 69 References 2 Figures

evelopment (XOD) principles and tool implementation to support ontology interoperability

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n Journal of Biomedical Semantics 9(1) · December 2018 with 180 Reads 
0169-2

e
Zuoshuang Xiang
niversity of Michigan

+2 Yu Lin Pheromone in baby mous

niversity of Pennsylvania 23.92 · University of Michigan interested in sex Read More

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to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and
developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies
representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee)
ects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar
d proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These
existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology
s), and involve community efforts to support new ontology development, promoting standardized and
d knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool
atly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible,
usable (i.e., FAIR).

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pporting software programs Ontofox retrieval of an NCBITaxon subset. Input data includes 3
species of organisms (human, mouse, and rat) and Ontofox…

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ournal of Biomedical Semantics (2018) 9:3

86/s13326-017-0169-2

EW Open A

eXtensible ontology development

D) principles and tool implementation
upport ontology interoperability
n He1* , Zuoshuang Xiang1, Jie Zheng2, Yu Lin3, James A. Overton 4 and Edison Ong5

act
gies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds
cal and biomedical ontologies developed, it has become critical to ensure ontology interoperability an
of interoperable ontologies for standardized data representation and integration. The suite of web-bas
imal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology developm
rizing the common features of Ontoanimal and other similar tools, we identified and proposed an “eXtensi
gy Development” (XOD) strategy and its associated four principles. These XOD principles reuse existing term
ic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), a
community efforts to support new ontology development, promoting standardized and interoperable data
dge representation and integration. The adoption of the XOD strategy, together with robust XOD tool
pment, will greatly support ontology interoperability and robust ontology applications to support data to be
e, Accessible, Interoperable and Reusable (i.e., FAIR).
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5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
p
rds:See all ›
Ontology, See all ›
Interoperability, See all
eXtensible ›
ontology development, Software, Ontoanimal
Download citation tools, Ontofox, Ont
Share Download full-text PDF
14 Citations 69 References 2 Figures
t, Semantic alignment, And ontology design pattern

ound OBO and non-OBO ontologies. Given hund

matics, an ontology is a set of computer- and
nterpretable terms and relations that represent
and their relations in a specific domain of the
Hundreds of biological/ biomedical ontologies
n developed in the last two decades. The Open
al and Biomedical Ontologies (OBO) Foundry is
orative initiative aimed at establishing a set of
development principles and incorporating
es following these principles in an evolving non-
nt and interoperable suite [1]. The OBO library
y includes over 160 ontologies covering >3 mil-
ms in biological and clinical domains. NCBO
l [2] has over 400 ontologies including both
dence: yongqunh@med.umich.edu
boratory Animal Medicine, Department of Microbiology and
y, Center for Computational Medicine and Bioinformatics,
f Michigan Medical School, Ann Arbor, MI, USA
uthor information is available at the end of the article
ontologies developed, a critical issue is the lack
ogy interoperability, preventing the seamless
standing and exchange of semantic information
different resources.
Ontologies are widely used in different area
including: (1) Naming “things”; (2) Knowledge b
struction, e.g., the Ontology of Vaccine Advers
(OVAE) representing the knowledge of advers
induced by FDA-licensed vaccines [5]; (3) D
change, e.g., BioPAX for representing molecular
lular pathways and facilitating the exchange of b
pathway data [6]; (4) Data integration, e.g., the Ont
Biomedical Investigations (OBI) [7] for in
representations of data in various areas of life-sci
clinical investigations; (5) Data analysis, as exemp
the wide usage of the Gene Ontology (GO) [8] to
high-throughput gene expression data analyses; (6
language processing [9, 10]; (7) Metadata standar
ation [11–13]. (8) Information retrieval and new kn
discovery [14–16].

© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a lin
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication w
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise

ournal of Biomedical Semantics (2018) 9:3 Pa

port various needs in ontology development and
ons, different software programs have been devel-
he Protégé OWL editor [17] is likely the most
tool for manual processing and editing of ontology
cuments. However, manual ontology development
lly tedious and inefficient, especially when the
of ontology is enormous. Over the years, we have
d a collection of web-based “Ontoanimal” tools
g Ontofox [18], Ontodog [19], Ontorat [20], Onto-
Ontobeep [22], Ontobull [23], Ontokiwi [24], and
[20]. Each Ontoanimal tool has its specific func-
d the collective use of these tools enables users to
he full development of ontology and linked
., data published on the Web that it is expli-
fined, machine-readable, and interlinked with
data sets [25]), including: extracting ontology
for term reuse and semantic alignment, pro-
ntology community views, adding and editing
ontology terms, visualizing and comparing
y terms, supporting community editing and
on, and creating ontology-based linked data.
k-end He group RDF triple store serves as
ault ontology RDF triple store for the OBO
https://www.researchgate.net/publication/322441127_The_eXtensible_ontology_development_XOD_principles_and_tool_implementation_to_su…
XOD: eXtensible ontology development
In information technology, extensible describe
thing (e.g., a program or protocol) that is des
that users/developers can expand or add to its
ities with no or minimal change in the system’s
structure and data flow. For example, extensib
primary feature of the eXtensible Markup L
(XML) system. Being “eXtensible”, XOD conta
key principles that are extensible at different
ontology development (Fig. 1):
(i) Ontology term reuse. Instead of reinventing
wheel when generating new ontologies, XOD
emphasizes the reuse of terms from existing
ontologies that are well constructed and com
used by the ontology community [1, 28, 29].
(ii) Ontology semantic alignment. For ontology
interoperability, it is important to align impo
terms from existing ontologies and newly ad
terms with the same semantics.
(iii) ODP usage for new term generation and
term editing. Instead of adding one term at
XOD emphasizes the addition or editing of a
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 5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
ault ontology RDF triple store for the OBO
See all › [21].See all › SeetoallProtégé,
› of terms based on ontology
ontologies Complementary
14 Citations 69 References 2 Figures
mal tools are widely used for efficient and
ontology development without requiring pro-
ng skills. For example, according to Google
s and Google Scholar, Ontobee has been used
77,000 users from 181 countries, Ontofox has
ed by over 17,000 users from 147 countries,
toanimal tools have been cited by >400 publi-
n the last 5 years.
Ontoanimal tools and other similar tools have
ntly enhanced the speed and quality of ontology
ment and improved ontology interoperability.
n increasing number of these tools, it would be
nt to identify the common features of these tools.
rospective examination and careful summary of
ols, we realized the most common feature of these
ng their support for “extensible” ontology develop-
ch extensibility is crucial to increase the interoper-
mong the ever increasing number of ontologies.
r, a systematic view of “extensible” ontology devel-
is not available. Thus, we propose the “eXtensible
y Development” (XOD) strategy and four XOD
s in this paper. Such an XOD strategy is comple-
to the OBO principles and the OBO goal of
g interoperable ontology suite [1], and it is also
mentary to the ten simple rules proposed for bio-
ontology development [26]. We also believe that
tion of the XOD strategy and principles support
R Guiding Principles proposal that all research data
e Findable, Accessible, Interoperable and Reusable
or both machine and human users [27].
ournal of Biomedical Semantics (2018) 9:3
https://www.researchgate.net/publication/322441127_The_eXtensible_ontology_development_XOD_principles_and_tool_implementation_to_su…
XOD emphasizes the addition or editing of a
Download citation design
Sharepatterns Download full-text PDF
(iv) Community extensibility. While the develop
an ontology might be initiated by a small gro
one or a few use cases, the ontology should
co-developed and applied to more use cases
people in a broader community.
Ontoanimal tools (Fig. 1) and many other p
support XOD principles (Table 1). In the f
sections, different principles and associated t
described with details.
XOD 1: Ontology term reuse
Reusing terms from reliable reference onto
better than reinventing the wheel to generate ne
in an ontology [18, 30]. The reference ontolog
be registered in an ontology library (e.g., OBO F
to make these terms more findable, accessi
reusable. To improve reusability and extensibilit
ogy terms in the reference ontologies should be
sive and generalizable and endure consistency
and evaluation. To maintain ontology interop
ontology term mapping is often used to map ter
different ontologies with the same meaning [31
pared to ontology term reuse, term mapping is l
since it is time-consuming, often inaccurate, re
and increases maintenance cost and confusio
multiple ontologies without using the ontolo
reuse strategy, ontology mapping becomes a c
for ontology interoperability [32]. The wide usa
Pa
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ummary of Ontoanimal tools and their features. Ontofoxsupports ontology reuse by extracting terms and axioms. Ontodog provides
community views by allowing community-preferred annotations. Ontorat automatically generates new ontology terms and edits ex
sed on ontology design patterns. Ontobee is an ontology linked data server for OBO library ontologies and many non-OBO ontolog
-based Ontobeep program supports ontology comparison and identification of redundant terms. Ontokiwi is a Wiki-like ontology ed
n program. Ontobedia is an application of Ontokiwi. Ontobat supports ontology-based data processing (e.g., conversion from Excel t
ysis. These tools support different XOD principles

use principle would make the mapping among
ontologies unneeded.
ial method of ontology term reuse was to import a
ogy, which was not ideal since it might import too
related terms. Instead of importing external ontol-
a whole, the Minimum Information to Reference
nal Ontology Term (MIREOT) strategy, introduced
developers [30], proposes the usage of the minimal
ion of an external ontology term that is of direct
o a target ontology [30]. Specifically, MIREOT sug-
following minimal set: (1) source ontology URI;
e term URI; and (3) target direct superclass URI.
set of information, the source ontology term can
ted to under the target direct superclass. Since it is
rd to maintain semantic consistency among ontol-
e popular MIREOT strategy provides a simple solu-
possible semantics loss.
Ontofox, Ontodog, and Ontobull support ter
Originally named OntoFox, Ontofox was the f
tool to support the MIREOT strategy (Fig.
Ontofox is able to quickly and easily fetch user-
terms and their annotations from source ontolo
assign them under defined superclass(es) in targ
ogies (Fig. 2a and b). Ontofox also extends MIE
retrieving semantical axioms with different opt
next section). Ontodog is also able to extract a
ontology terms and axioms [19]. Unlike plain te
ition in Ontofox, Ontodog uses Excel input files
tify terms to retrieve. To match possible up
source ontologies, e.g., the upper-level Basic
Ontology (BFO) [33], Ontobull is developed f
matic conversion and updating [23].
Several other tools also support ontology ter
(Table 1). The Protégé MIREOT plugin [

XOD principles and supporting software programs

ple # XOD principle names Tool name
Ontology term reuse Ontodog, Ontofox, OntoMATON, Protégé MIREOT plug
Semantic alignment Ontobeep, Ontofox, ROBOT
ODP usage MappingMaster, Ontorat, Populous, ROBOT, TermGenie
Community extensibility Ontodog, Ontokiwi/Ontobedia, WebProtege

ournal of Biomedical Semantics (2018) 9:3 Pa

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ntofox retrieval of an NCBITaxon subset. Input data includes 3 species of organisms (human, mouse, and rat) and Ontofox settings. T
settings can be entered viaweb-based forms (a). The Ontofox results can be shown using Protégé (b-d). Different results may appe
ent settings: The setting “IncludeNoIntermediates” implements MIREOT (b). The setting “includeComputedIntermediates” extracts compu
iates which that are closest ancestors of more than one low level source terms (c). The setting “includeAllIntermediates” outputs all
ntermediates

ton [35] support term reuse as a plugin of the
OWL editor or Google Spreadsheets, respect-
OBOT is a command-line Java tool supporting
action of ontology terms and subsets [36].
also has many other features and supports mul-
D principles (Table 1) as described below [36].
tter support ontology reuse and community-
ntology development, it would also be valuable
the authors of the source ontology know of the
a term in their ontology. The Ontobee program
udes a feature in the web page of an ontology
at shows all the other ontologies reusing the
hich supports ontology interoperability.
Ontology semantic alignment
D 2 principle proposes to align imported ontol-
ms and newly added terms with the same or
ble semantics. Such semantic alignment has two
meanings. First, in addition to the term reuse in
the semantic relations among reused terms
also be reused and aligned. If different relation
e., object properties) mean the same thing, they
be merged. Correspondingly, the axioms of
reused terms and any additional terms specifie
axioms should also be retrieved and imported.
the semantics related to newly developed term
be aligned and compatible with imported seman
the same or compatible relations be used in
ontology. If a well-defined relation already ex
should reuse the relation instead of defining
relation with the same meaning. Such semant
ments support ontology semantic interoperabilit
Ontofox and Ontodog support ontology
alignment. Ontofox and Ontodog extract sema
ioms and terms related to user-specified terms
source ontologies. Given different options, On
lows the computation and extraction of (i) inte
terms that are the shared parent terms of mul
level terms (Fig. 2c), or (ii) all intermediate te
tween the required terms and a top level term
These subset semantic axioms and terms can
retrieved and become a part of the new ontolo
that manual intervention and judgment may
needed now to ensure the semantic alignment
retrieved subset and target ontology semantics
will also be important to have computer-su

ournal of Biomedical Semantics (2018) 9:3 Pa

capture and synchronization of ontology evolu-
updates. To foster reliability, an overall formal
n and consistency checking would be needed.
ODP-based ontology development
tology Design Pattern (ODP) represents a
solution to solve a recurrent modeling problem
context of ontology engineering [20, 38, 39].
an example of using Ontorat to add new term
tations, and axioms to the Ontology of
Events (OAE) [40]. Ontorat uses reusabl
(Fig. 4a) to automatically generate and edit
terms and axioms and provides term annota
specific ODP can be used to derive an Excel
of different terms/annotations and a set of ru
define the relations among those terms/ann

rovide extensible representations of entities and (Fig. 3b). The Ontorat template, similar to
, make ontologies more maintainable, and im- (Quick Term Template) originated by OBI de
ntology quality. This XOD 3 principle requires [41], can be populated with specific terms or
-based strategy to develop and edit new terms, tions to define or annotate specific ontology t
ons, and relations. This principle extends XOD generate axioms illustrating logic relations
XOD 2 d id ifi f ibl d l Wi h h f h
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5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
XOD 2 and provides a specific, feasible, and ontology terms. With the support of the
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14 Citationsto achieve interoperable
69 References ontology
2 Figures settings (Fig. 3c), the populated
neration/annotation and semantic consistency. can then be converted into an OWL file wit
Ontorat program (http://ontorat.hegroup.org) generated ontology terms and axioms (Fig. 3d
ODP-based creation of new ontology terms, The setting and template files can also be sa
ons and logical axioms [20]. Fig. 3 illustrates reused.

ew OAE term generation and annotation using Ontorat. First an ODP was identified to define new AE terms (a). The ODP guide
on of an Excel template and Ontorat settings. The template file was populated with detailed contents (one row for one new ter
s shown in this example) (b). The Ontorat settings were matched to the Excel data format (c). The settings and populated Excel
d as Ontorat inputs to generate an OWL format output file containing newly created ontology terms together with their annota
ut could be displayed using the Protégé OWL editor (d). After merging the output file to existing OAE file, the detailed informa
ontology terms (e.g., ‘discomfort AE’ OAE_000081) seen in (d) will be obtained from and aligned to existing OAE (e)

ournal of Biomedical Semantics (2018) 9:3 Pa

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14 Citations 69 References 2 Figures
general ontology development pipeline using XOD principles. To initiate a new ontology, needed terms from existing ontologie
and reused (XOD 1) and aligned together with other ontology terms in a consistent semantic framework (XOD 2). To add mor
antics afterwards, we can use the same XOD 1/2 methods to add terms from existing ontologies, and for new terms, we can eit
ed term generation strategy (XOD 3) and manually align and add terms to the new ontology. Community extensibility (XOD 4)
dered and applied during the whole ontology development pipeline

ODP-based XOD tools include MappingMaster
rmGenie [43], Populous [44], Webulous [45],
BOT [36] (Table 1). Developed as a Protégé plu-
ppingMaster can only be used with old version
3.4 and is not available for newer Protégé 4 and 5
rgeting domain experts, TermGenie provides a
lication that supports new GO term generation
n predefined patterns [43]. Populous requires soft-
stallation but provides a user-friendly interface
bulous is Google Add-On application usable with
Spreadsheets [45]. ROBOT also has a template
or converting spreadsheets of terms to OWL files.
ommunity extensibility
mmunity’s involvement during the developing
an ontology is the key for wide adoption of the
in the future. However, this step is often a
ck for ontology development, since the wider
munity is, the more difficult it is to reach agree-
n term definitions and classifications. In the
an ontology is often initiated by a small group
n driven by one or more use cases. To enhance
ty and broad recognition, XOD 4 recommends
roader community with more developers and
articipate in the ontology development and
ons. This XOD community extensibility
emphasizes the community participation to
xtend, develop, and apply an ontology. With the
of community extensibility, one ontology can
ded to cover different use cases in the same pro-
different projects from a wide range of research
nities. The nature of such a practice will require
ople to participate, make the ontology commu-
er, and achieve better data interoperability.
otege [46] and Ontokiwi [24] support community-
ntology development. WebProtege is a web-based
editor that supports collaborative OWL ontology
development [46]. WebProtege has been used
groups. It includes full change tracking and revisio
and many community collaboration features
sharing and permissions, threaded notes and dis
watches and email notifications. Ontokiwi is t
friendly Wiki-like web program that supports com
wide ontology editing, annotation, discussion, and
tion [24]. Ontobedia is an Ontokiwi application p
with existing biomedical ontologies [24]. Th
like addition and editing of text that is not
the ontology makes Ontokiwi/Ontobedia a unique
for community-wide ontology discussion and distr
For community-wide ontology development and
tions, tools to support ontology query, compari
evaluations are also needed. NCBO BioPortal [2], O
Ontobee [21], and AberOWL [48] are commo
ontology registry and repositories that also provi
ogy visualization, queries and analysis features, wh
tates the community involvement principle. Th
ontology toolkit (http://www.ebi.ac.uk/spot/ontolo
provides a list of community-driven open source
tools. For example, Ontobee (http://www.ontobee.
ontology browser and a linked ontology data s
dereferencing ontology terms [21]. Ontobeep is an
comparison program that compares ontologies an
fies common terms existing in two or three onto
aligning 2–3 ontologies from the roots of these o
[22]. Ontobeep also detects inconsistency and term
tion in one or more ontologies.
Demonstrations of XOD implementation for interop
ontology development
Figure 4 outlines a simple pipeline of how t
principles can be used together for productive
development. Basically, a new ontology can be
by reusing existing terms from different o
(XOD 1) and aligning these terms in a

ournal of Biomedical Semantics (2018) 9:3 Pa

rk (XOD 2), and new terms can be added by ex- retrieved from the US Department of Ag
the semantic framework (XOD 2) and if ODPs (USDA) and other public databases the inform
ble, applying ODP-based approach (XOD 3). approximately 800 licensed animal vaccines. M
y development often uses top-down and adding these animal vaccines to VO would
up approaches simultaneously [49]. The ontol- consuming. To speed up the inclusion of t
ation step is usually achieved by the top-down number of licensed animal vaccines to VO, an O
h, i.e., developing the top level semantic frame- developed to include different entities (e.g.,
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5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
reusing
See all › and aligning
See all ›upper level
Seeterms
all › and
s from existing ontologies (XOD 1/2). The same
14 Citations 69 References 2 Figures
n approach can also be used to generate the
vel new terms commonly identified in the new
. Meanwhile, the bottom-up approach is use
ven and focuses on adding new terms to address
use cases. For the bottom-up approach, XOD 1–
ples are all important, and if possible, ODP-
sign and term generation (XOD 3) is often crit-
nsure development efficiency and consistency.
we will demonstrate our pipeline by using the
e use case of developing the community-based
Ontology (VO) [10, 50, 51]. As outlined in the
e ontology development pipeline (Fig. 4), at the
ge of the VO development, we performed ontol-
ey and reused terms from several existing ontol-
cluding BFO [33], OBI [7], GO [8], and the
tion Artifact Ontology (IAO) [52]. The original
ion reported in 2009 included ~1000 imported
rom 10 existing ontologies and ~1000 VO-
terms [50]. Since then more terms have been
o VO. As of November 20, 2017, out of 6541
VO, approximately 1600 terms were imported
sed from approximately 30 ontologies (http://
tobee.org/ontostat/VO).
VO-specific terms were added to VO by seman-
ignment with the upper BFO ontology or middle
ologies (e.g., OBI) (XOD 2). For example, VO
ccine’ (VO_0000001) is asserted as a subclass of
m ‘processed material’ (OBI_0000047). This
n means that any non-processed material (e.g.,
ious bacterium that exists in the air) that causes
tion in human and eventual immune responses
ection in the human is not counted as a vaccine.
y, the VO term ‘vaccination’ (VO_0000002) is
as a subclass of OBI term ‘administering
e in vivo’ (OBI_0600007). The alignment with
tering substance in vivo’ differentiates VO
on (i.e., administering a vaccine to in vivo) from
zation (i.e., to make one immune to something).
arison, vaccination is considered as the synonym
nization in MedDRA, a controlled terminology
ommonly used for representation of regulatory
[53].
ny cases, we can generate a number of new
multaneously by developing and following spe-
Ps (XOD 3). For example, the VO developers
ournal of Biomedical Semantics (2018) 9:3
s of ontologies developed now, it is critical to
ntology interoperability, and the XOD principles
a practical solution. Given the importance of
es in the integration, sharing, and analysis of the
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name, manufacturer, animal species, animal p
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and disease), annotations, Share
and the semantic Download full-text PDF
among these entities. Such an ODP was further
design an Excel template which was then ap
include the categorized information of these
Ontorat was finally used to automatically tran
ODP and the information recorded in the Exc
an OWL file and then imported to VO [20].
more, the same ODP could be used later to
animal vaccines to VO. The Ontorat use case
based VO addition of veterinary vaccines w
presented in the 2012 International Confere
Biomedical Ontology (ICBO) [54]. Since the
ODPs were also developed for further VO deve
[51]. Meanwhile, it is noted that not all new te
be fit under identifiable common design pattern
case, we can generate the term by aligning it w
ing framework (XOD 2) (Fig. 4).
As a community-based open source ontology
development has involved the broader commun
continuous development (XOD 4). The co
participation helps further extend the VO and
operability with other biomedical ontologies. For
according to BioPortal and Ontobee, the VO term
(VO_0000001) has been reused by more than ten
tologies such as OBI and Apollo Structured V
(https://github.com/apollodev/), and the VO term
ation (VO_0000002) has been reused by ten other o
such as the Prescription of Drugs Ontology (https:
com/OpenLHS/PDRO). In addition, the VO comm
volvement makes it achieve better data interoperab
other ontologies. Meanwhile, the community inv
extends the applications of VO, such as vaccine-rela
and B cell response analysis and queries [55], epi
management [56], vaccine-related literature mining
vaccine-related network analysis [57, 58].
In addition to VO, many other ontologies, e.g.,
Genomics Ontology (BCGO) [37], MicrO onto
representing microorganism phenotypic and m
characters [59], and BioAssay Ontology (BAO) [
been developed using the same or similar strategie
Discussion and perspectives
The XOD strategy and principles reflect the grow
turity of biological and biomedical ontology deve
When only a small number of ontologies were de
such XOD strategy was not needed. Howev
Pa
interoperable, and reusable queries of the un
data from these databases. Therefore, the XOD
supports the eventual achievement of the FAI
data.
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5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
g g y
ng large and
See all › heterogeneous
See all › data/metadata
See all › and Many challenges exist in adopting and achie
ge, 14theCitations
XOD strategy is very significant
69 References 2 Figures and goals defined inDownload
the XOD citation
strategyShare
and principl Download full-text PDF
o meet the challenges in the current big data era. the interoperability among current hundreds o
g the four XOD principles, the first three princi- ogies is still limited and challenging [32, 62, 63
phasize the requirements to reuse ontology redundancy among ontologies cannot be solve
xtend and align semantic structures, and build leading to issues of achieving data FAIRness.
ms and semantics among terms using design pat- only a small amount of data resources (includin
OD 2 is a more general principle which covers number of databases) adopt ontology-guided
antic interoperability among terms including which restricts data interoperability and analysi
om the target ontology and terms newly gener- while many linked data systems [25] standard
mported from source ontology. Extending XOD using ontologies, the ontologies underlying linked
, XOD 3 provides a more specific mechanism often non-interoperable, making linked data
P-based term generation and editing) to achieve become individual silos and difficult to integrate
nt ontology term generation and annotation. To address these challenges, it is important to a
he first three principles provide more technical XOD strategy and XOD principles. Active ontolo
e, XOD 4 emphasizes the community collabor- ing and outreach will be beneficial.
d involvement in new ontology development. The suite of Ontoanimal tools has provided
s complementary to the OBO principles [1] and features to address several real issues in ontolog
simple rules proposed for ontology development opment. Each of these tools focuses on one
e OBO principles (e.g., open, common format, ver- primary tasks, and all together they are com
scope, relations, users, collaboration, and locus of strongly support XOD principles. Given the co
) provide general principles for the development of these tools, there are concerns about their
ntology (http://obofoundry.org/principles/fp-000- and sustainability. Since these tools are mor
y.html). The ten simple rules proposed by Malone research in ontology development, it is impo
clude ontology term reuse, design patterns, and have a strong evaluation system to be used t
ity engagement [26], which are directly associated understand the strengths and limitation of each
D principles. The other 7 rules (e.g., scope, license, While Ontoanimal tools and other similar XO
g) are not directly related. In comparison to the have already supported the XOD strategy, exist
nciples and the ten simple rules, the XOD princi- require further improvements, and more user
ess the single important point of ontology extensi- integrative tools are needed. Tools are critical
d emphasize different scales of extensible relations more efficient extensible ontology developm
ntologies, with the aim to achieve ontology inter- example, although it was recognized that term r
ty. Since different ontologies extend and are a better strategy, the term reuse principle was no
with existing reliable ontologies, applying the XOD implemented until Ontofox and other tools we
s will support the OBO aim of establishing non- oped. Currently XOD tool usage often requires e
nt and interoperable suite of ontologies. training. More easy-to-use and integrative XO
OD strategy supports the FAIR Guiding Princi- are desired for ontology developers and users wi
hich propose that various data be Findable, limited programming background. We believe
le, Interoperable and Reusable [27]. Ontologies adoption of the XOD principles together with
the basic foundation for the data FAIRness. XOD tools would greatly support interoperable
g the XOD strategy will lead to the development development and data FAIRness.
sible ontologies and the generation of ontology-
d data and metadata representations. Such Conclusion
-supported data sharing and integration will Our examination of Ontoanimal tools and similar
natural data access, interoperability, and usabil- discovered their shared features of extensibility.
ry, and advanced analysis. For example, the posed the “eXtensible Ontology Development” (XO
knowledge base uses the OBO ontologies to se- egy and four XOD principles to support extensible
ly integrate data from 18 prominent biomedical development and usage. We propose to adopt th
s [61]. Millions of RDF triples were also gener- principles for active development and usage of e
n KaBOB, enabling findable, accessible, ontologies and tools, leading to better data FAIRnes

ournal of Biomedical Semantics (2018) 9:3 Pa

ons 5. Marcos E, Zhao B, He Y. The ontology of vaccine adverse events

https://www.researchgate.net/publication/322441127_The_eXtensible_ontology_development_XOD_principles_and_tool_implementation_to_s… 10/17
5/14/2020 (PDF) The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
ormal ontology; GO: Gene ontology; MIREOT: Minimum
See all › See all › See all ›
to reference an external ontology term; NCBO: National Center
14 Citations 69 References 2 Figures
cal Ontology; OAE: Ontology of adverse events; OBO: Open
nd biomedical ontologies; ODP: Ontology design pattern;
ontology language; RDF: Resource description framework;
sible markup language; XOD: eXtensible ontology development
gements
edge the OBO Foundry consortium and OBO ontology
for their support and collaborations.
imal tool research was partly supported by the NIH National
Allergy and Infectious Diseases grant 1R01AI081062.
y of data and materials
ble.
ontributions
mal tool project design and management, initial XOD concept
reparation of the first manuscript draft; ZX Primary developers of
tools Ontofox, early version of Ontobee, Ontobeep, Ontodog,
d Ontobat; JZ Co-developer of Ontodog, Ontorat, and Ontobee;
mal tool testing, discussion, and evaluation; JO ROBOT tool
Ontoanimal tool testing and evaluation; EQ Primary developers of
ntobedia, later version of Ontobee, Ontobull, and Ontoanimal
nance. All authors participated in discussion, manuscript
and editing, and approved the manuscript.
roval and consent to participate
ble.
r publication
ble.
interests
declare that they have no competing interests.
er’s Note
ture remains neutral with regard to jurisdictional claims in
maps and institutional affiliations.
ails
boratory Animal Medicine, Department of Microbiology and
y, Center for Computational Medicine and Bioinformatics,
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