The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation an...

Full description

Saved in:
Bibliographic Details
Published inJournal of biomedical semantics Vol. 9; no. 1; pp. 3 - 10
Main Authors He, Yongqun, Xiang, Zuoshuang, Zheng, Jie, Lin, Yu, Overton, James A., Ong, Edison
Format Journal Article
LanguageEnglish
Published London BioMed Central 12.01.2018
BioMed Central Ltd
BMC
Subjects
Algorithms
Analysis
Bioinformatics
Biological Ontologies
Combinatorial Libraries
Computational Biology/Bioinformatics
Computational linguistics
Computer Appl. in Life Sciences
Data Mining and Knowledge Discovery
eXtensible ontology development
Interoperability
Language processing
Mathematics
Mathematics and Statistics
Natural language interfaces
Ontoanimal tools
Ontofox
Ontology
Review
Semantics
Software
Ontorat
And ontology design pattern
Ontology
Ontoanimal tools
Software
eXtensible ontology development
Ontofox
Interoperability
Ontobee
Semantic alignment
Online AccessGet full text
ISSN2041-1480
2041-1480
DOI10.1186/s13326-017-0169-2

Cover

Abstract Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an “eXtensible Ontology Development” (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).
AbstractList Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an “eXtensible Ontology Development” (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).
Abstract Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an “eXtensible Ontology Development” (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).
ArticleNumber 3
Audience Academic
Author Xiang, Zuoshuang
Lin, Yu
Ong, Edison
Zheng, Jie
He, Yongqun
Overton, James A.
Author_xml – sequence: 1
  givenname: Yongqun
  orcidid: 0000-0001-9189-9661
  surname: He
  fullname: He, Yongqun
  email: yongqunh@med.umich.edu
  organization: Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School
– sequence: 2
  givenname: Zuoshuang
  surname: Xiang
  fullname: Xiang, Zuoshuang
  organization: Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School
– sequence: 3
  givenname: Jie
  surname: Zheng
  fullname: Zheng, Jie
  organization: Department of Genetics, University of Pennsylvania Perelman School of Medicine
– sequence: 4
  givenname: Yu
  surname: Lin
  fullname: Lin, Yu
  organization: Center for Computational Science, University of Miami
– sequence: 5
  givenname: James A.
  surname: Overton
  fullname: Overton, James A.
  organization: Knocean Inc
– sequence: 6
  givenname: Edison
  surname: Ong
  fullname: Ong, Edison
  organization: Department of Computational Medicine and Bioinformatics, University of Michigan Medical School
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29329592$$D View this record in MEDLINE/PubMed
BookMark eNp9kktr3DAUhU1JaR7ND-imGLpJF0718kObQkibNhDIJoXshCxfTTTIkiNpAvPvI9dJmyklFkby1Tkf9-JzWOw576AoPmB0inHXfImYUtJUCLf5bXhF3hQHBDFcYdahvRfn_eI4xjXKD6UYdfRdsU84Jbzm5KC4v7mDEm4TuGh6C6V3yVu_2pYDPID10wgulSe3198-l1MwTpnJQiylG8rkvS3NmL9njUzGu1wr42aafEh_QcYlCH6CIHtjTdq-L95qaSMcP-1Hxa-L7zfnP6ur6x-X52dXlarbOlWaSMgDdpowBqAHKgnpFWEKKYUYaxDXPeoVb4BIkjcMkvaUgJSqloxxelRcLtzBy7XIzY8ybIWXRvwu-LASMiSjLAiu1QAtrfEAktWUdQw6rYea1IqRnurM-rqwpk0_wqDywEHaHejujTN3YuUfRN02ddOQDDh5AgR_v4GYxGiiAmulA7-JAvOOZy0nc9-fFulK5taM0z4T1SwXZzUhLactm4Gn_1HlNcBoVE6KNrm-Y_j4coQ_vT9HIQvaRaCCjzGAFsosvzWTjRUYiTl3YsmdyLkTc-7E7MT_OJ_hr3nI4olzrFYQxNpvgsuBeMX0CMIO7CM
CitedBy_id crossref_primary_10_3389_frai_2025_1508225
crossref_primary_10_3390_bdcc7020109
crossref_primary_10_1093_bfgp_elab029
crossref_primary_10_12688_wellcomeopenres_15904_1
crossref_primary_10_1152_physiolgenomics_00104_2020
crossref_primary_10_1186_s12911_023_02182_8
crossref_primary_10_3389_fdata_2022_998648
crossref_primary_10_3389_fimmu_2022_1066733
crossref_primary_10_1186_s12859_019_3194_6
crossref_primary_10_1016_j_procs_2023_10_123
crossref_primary_10_1186_s13326_019_0217_1
crossref_primary_10_1016_j_procs_2023_01_306
crossref_primary_10_12688_wellcomeopenres_21252_1
crossref_primary_10_1186_s13326_024_00302_5
crossref_primary_10_3390_pharmaceutics15061673
crossref_primary_10_1186_s13326_023_00300_z
crossref_primary_10_1038_s41597_020_0523_6
crossref_primary_10_1016_j_procs_2021_12_010
crossref_primary_10_1109_OJCOMS_2024_3371871
crossref_primary_10_1162_dint_a_00255
crossref_primary_10_1186_s13326_022_00279_z
crossref_primary_10_3390_app9224936
crossref_primary_10_1093_database_baac087
crossref_primary_10_1093_jamia_ocz125
crossref_primary_10_1016_j_eswa_2023_120239
crossref_primary_10_12688_wellcomeopenres_19363_2
crossref_primary_10_12688_wellcomeopenres_19363_1
crossref_primary_10_12688_wellcomeopenres_19899_1
crossref_primary_10_1016_j_matdes_2023_112603
crossref_primary_10_1186_s12859_021_04402_2
crossref_primary_10_1186_s13326_025_00327_4
crossref_primary_10_1186_s12859_019_3191_9
crossref_primary_10_1371_journal_pone_0295541
crossref_primary_10_12688_wellcomeopenres_19489_1
crossref_primary_10_12688_wellcomeopenres_22788_1
crossref_primary_10_12688_wellcomeopenres_19489_2
crossref_primary_10_3389_fcimb_2025_1509226
crossref_primary_10_3390_fi15100331
crossref_primary_10_1186_s12859_019_3002_3
crossref_primary_10_1186_s13326_021_00250_4
crossref_primary_10_3389_fphar_2019_00415
crossref_primary_10_1186_s12859_019_2729_1
crossref_primary_10_3233_SW_223096
crossref_primary_10_1016_j_jbi_2022_104007
crossref_primary_10_3389_fphar_2019_00975
crossref_primary_10_1093_nar_gky999
crossref_primary_10_3897_BDJ_12_e128585
crossref_primary_10_3233_SW_233458
crossref_primary_10_12688_wellcomeopenres_16682_1
crossref_primary_10_1155_2021_6637810
crossref_primary_10_1038_s41597_021_01112_5
crossref_primary_10_12688_wellcomeopenres_20701_2
crossref_primary_10_12688_wellcomeopenres_20701_1
crossref_primary_10_1016_j_cotox_2019_09_001
Cites_doi 10.1186/1471-2105-15-S14-S4
10.1093/database/bav010
10.1186/2041-1480-2-S2-S8
10.2165/00002018-199920020-00002
10.3233/AO-2011-0086
10.1371/journal.pone.0099979
10.1186/1471-2105-9-S5-S1
10.1186/s13326-016-0090-0
10.1093/bioinformatics/btu256
10.1007/s10278-007-9065-0
10.4258/hir.2013.19.4.235
10.1186/2041-1480-5-48
10.3233/SW-2010-0014
10.1038/75556
10.1038/sdata.2016.18
10.1038/nbt.1666
10.1093/bioinformatics/bts718
10.1186/s13040-014-0036-y
10.1093/bib/bbv011
10.1371/journal.pcbi.1004743
10.1093/bioinformatics/btu008
10.1016/j.future.2010.10.011
10.1093/nar/gkw918
10.1371/journal.pone.0154556
10.1093/bib/bbs053
10.3233/AO-2011-0087
10.1186/2041-1480-3-17
10.1186/s13326-016-0060-6
10.1038/npre.2009.3553
10.1186/2041-1480-4-S1-S6
10.1093/nar/gkr469
10.1186/s12859-015-0559-3
10.1186/2041-1480-5-S1-S5
10.1186/s13326-016-0100-2
10.7551/mitpress/9780262527811.001.0001
10.1186/s13326-016-0069-x
10.1186/s13326-016-0055-3
10.1038/nbt1346
10.1186/2041-1480-6-4
10.1093/nar/gki470
10.1007/s40495-016-0055-0
10.1093/database/bar045
10.1007/978-3-642-22630-4_6
10.1186/2041-1480-5-29
10.1186/1471-2105-13-S1-S5
10.1145/2890489
10.1186/2041-1480-4-40
10.4018/jswis.2009081901
10.1186/2041-1480-4-33
10.1093/nar/gkq331
10.1186/2041-1480-2-S5-S1
10.1017/S0269888903000651
ContentType Journal Article
Copyright The Author(s). 2018
COPYRIGHT 2018 BioMed Central Ltd.
Copyright_xml – notice: The Author(s). 2018
– notice: COPYRIGHT 2018 BioMed Central Ltd.
DBID C6C
AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
7X8
5PM
DOA
DOI 10.1186/s13326-017-0169-2
DatabaseName Springer Nature Open Access Journals
CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
MEDLINE - Academic
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
MEDLINE - Academic
DatabaseTitleList

MEDLINE - Academic

MEDLINE
Database_xml – sequence: 1
  dbid: C6C
  name: Springer Nature OA Free Journals
  url: http://www.springeropen.com/
  sourceTypes: Publisher
– sequence: 2
  dbid: DOA
  name: DOAJ Directory of Open Access Journals
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 3
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 4
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
Discipline Languages & Literatures
Mathematics
EISSN 2041-1480
EndPage 10
ExternalDocumentID oai_doaj_org_article_9fcde7351dea453484e8ffd525c42b3f
PMC5765662
A522793742
29329592
10_1186_s13326_017_0169_2
Genre Journal Article
Review
Research Support, N.I.H., Extramural
GrantInformation_xml – fundername: National Institute of Allergy and Infectious Diseases
  grantid: 1R01AI081062
  funderid: http://dx.doi.org/10.13039/100000060
– fundername: NIAID NIH HHS
  grantid: R01 AI081062
– fundername: ;
  grantid: 1R01AI081062
GroupedDBID 0R~
53G
5VS
7X7
88E
8FE
8FG
8FH
8FI
8FJ
AAFWJ
AAJSJ
AASML
ABDBF
ABJCF
ABUWG
ACGFO
ACGFS
ACIWK
ACPRK
ACUHS
ADBBV
ADRAZ
ADUKV
AEGXH
AENEX
AFKRA
AFPKN
AHBYD
AHYZX
AIAGR
ALMA_UNASSIGNED_HOLDINGS
AMKLP
AMTXH
AOIJS
BAPOH
BAWUL
BBNVY
BCNDV
BENPR
BFQNJ
BGLVJ
BHPHI
BMC
BPHCQ
BVXVI
C6C
CCPQU
DIK
E3Z
EBD
EBLON
EBS
EJD
ESX
F5P
FYUFA
GROUPED_DOAJ
GX1
H13
HCIFZ
HMCUK
HYE
IAO
IEA
IHR
INH
INR
ITC
KQ8
L6V
LK8
M1P
M48
M7P
M7S
ML~
M~E
O5R
O5S
OK1
PGMZT
PHGZM
PHGZT
PIMPY
PJZUB
PPXIY
PQGLB
PQQKQ
PROAC
PSQYO
PTHSS
PUEGO
RBZ
RNS
ROL
RPM
RSV
SMT
SOJ
TUS
UKHRP
AAYXX
ALIPV
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
PMFND
7X8
5PM
ID FETCH-LOGICAL-c575t-f2ae3328f244eefd3a22bc24c0cc044609fb0bc96e2a2c961ea3b32eaac5a4493
IEDL.DBID M48
ISSN 2041-1480
IngestDate Wed Aug 27 01:25:08 EDT 2025
Thu Aug 21 14:06:49 EDT 2025
Fri Sep 05 01:25:47 EDT 2025
Tue Jun 17 21:14:56 EDT 2025
Tue Jun 10 20:12:35 EDT 2025
Thu Apr 03 07:02:00 EDT 2025
Tue Jul 01 03:54:47 EDT 2025
Thu Apr 24 22:56:06 EDT 2025
Sat Sep 06 07:20:56 EDT 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 1
Keywords Ontorat
And ontology design pattern
Ontology
Ontoanimal tools
Software
eXtensible ontology development
Ontofox
Interoperability
Ontobee
Semantic alignment
Language English
License Open AccessThis 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 link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c575t-f2ae3328f244eefd3a22bc24c0cc044609fb0bc96e2a2c961ea3b32eaac5a4493
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
ObjectType-Review-3
content type line 23
ORCID 0000-0001-9189-9661
OpenAccessLink https://doi.org/10.1186/s13326-017-0169-2
PMID 29329592
PQID 1989576929
PQPubID 23479
PageCount 10
ParticipantIDs doaj_primary_oai_doaj_org_article_9fcde7351dea453484e8ffd525c42b3f
pubmedcentral_primary_oai_pubmedcentral_nih_gov_5765662
proquest_miscellaneous_1989576929
gale_infotracmisc_A522793742
gale_infotracacademiconefile_A522793742
pubmed_primary_29329592
crossref_citationtrail_10_1186_s13326_017_0169_2
crossref_primary_10_1186_s13326_017_0169_2
springer_journals_10_1186_s13326_017_0169_2
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2018-01-12
PublicationDateYYYYMMDD 2018-01-12
PublicationDate_xml – month: 01
  year: 2018
  text: 2018-01-12
  day: 12
PublicationDecade 2010
PublicationPlace London
PublicationPlace_xml – name: London
– name: England
PublicationTitle Journal of biomedical semantics
PublicationTitleAbbrev J Biomed Semant
PublicationTitleAlternate J Biomed Semantics
PublicationYear 2018
Publisher BioMed Central
BioMed Central Ltd
BMC
Publisher_xml – name: BioMed Central
– name: BioMed Central Ltd
– name: BMC
References Y Kalfoglou (169_CR31) 2003; 18
A Guo (169_CR14) 2016; 7
H Dietze (169_CR43) 2014; 5
P Rocca-Serra (169_CR41) 2011; 6
VG Dugan (169_CR13) 2014; 9
A Bandrowski (169_CR7) 2016; 11
E Ong (169_CR24) 2016; 2016
J Malone (169_CR28) 2016; 12
Y He (169_CR15) 2016; 2
J Zheng (169_CR19) 2014; 30
R Hoehndorf (169_CR39) 2011; 2
169_CR4
R Cote (169_CR47) 2010; 38
M Horridge (169_CR46) 2014; 30
MD Wilkinson (169_CR27) 2016; 3
M O’Connor (169_CR42) 2010
E Maguire (169_CR35) 2013; 29
EG Brown (169_CR53) 1999; 20
Y Lin (169_CR51) 2012; 3
169_CR54
169_CR12
A Gonzalez-Beltran (169_CR11) 2014; 15
A Ozgur (169_CR10) 2011; 2
Y He (169_CR40) 2014; 5
CE Blank (169_CR59) 2016; 7
E Demir (169_CR6) 2010; 28
169_CR50
169_CR52
Z Xiang (169_CR18) 2010; 3
L Slater (169_CR48) 2016; 7
KM Livingston (169_CR61) 2015; 16
ME Aranguren (169_CR38) 2008; 9
E Marcos (169_CR5) 2013; 4
JL Chung (169_CR56) 2010; 2010
S Jupp (169_CR45) 2016; 7
Z Xiang (169_CR20) 2015; 6
169_CR22
169_CR23
S Abeyruwan (169_CR60) 2014; 5
B Smith (169_CR1) 2007; 25
E Hyvönen (169_CR62) 2010; 1
169_CR26
R Arp (169_CR33) 2015
S Schulz (169_CR3) 2013; 19
Y Zhang (169_CR58) 2013; 4
R Hoehndorf (169_CR29) 2013; 14
S Jupp (169_CR44) 2012; 13
169_CR63
J Zheng (169_CR49) 2016; 7
A Bernstein (169_CR65) 2016; 59
C Bizer (169_CR25) 2009; 5
PL Whetzel (169_CR2) 2011; 39
M Ashburner (169_CR8) 2000; 25
J Zheng (169_CR37) 2013; 1060
J Zheng (169_CR16) 2011; 2011
C Tao (169_CR57) 2014; 7
169_CR32
169_CR34
M Courtot (169_CR30) 2011; 6
R Vita (169_CR55) 2013; 4
E Ong (169_CR21) 2017; 45
169_CR36
L Ding (169_CR64) 2011; 27
DL Rubin (169_CR17) 2007; 20
A Doms (169_CR9) 2005; 33
References_xml – volume: 15
  start-page: S4
  issue: Suppl 14
  year: 2014
  ident: 169_CR11
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-15-S14-S4
– ident: 169_CR12
  doi: 10.1093/database/bav010
– volume: 2
  start-page: S8
  issue: Suppl 2
  year: 2011
  ident: 169_CR10
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-2-S2-S8
– volume: 3
  start-page: 1
  issue: 175
  year: 2010
  ident: 169_CR18
  publication-title: BMC Res Notes
– volume: 20
  start-page: 109
  issue: 2
  year: 1999
  ident: 169_CR53
  publication-title: Drug Saf
  doi: 10.2165/00002018-199920020-00002
– volume: 2016
  start-page: 65
  year: 2016
  ident: 169_CR24
  publication-title: AMIA Jt Summits Transl Sci Proc
– volume: 6
  start-page: 13
  issue: 1
  year: 2011
  ident: 169_CR41
  publication-title: Appl Ontol
  doi: 10.3233/AO-2011-0086
– volume: 9
  start-page: e99979
  issue: 6
  year: 2014
  ident: 169_CR13
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0099979
– volume: 9
  start-page: S1
  issue: Suppl 5
  year: 2008
  ident: 169_CR38
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-9-S5-S1
– volume: 7
  start-page: 49
  issue: 1
  year: 2016
  ident: 169_CR48
  publication-title: J Biomed Semantics
  doi: 10.1186/s13326-016-0090-0
– volume: 30
  start-page: 2384
  issue: 16
  year: 2014
  ident: 169_CR46
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu256
– volume: 20
  start-page: 34
  issue: Suppl 1
  year: 2007
  ident: 169_CR17
  publication-title: J Digit Imaging
  doi: 10.1007/s10278-007-9065-0
– ident: 169_CR54
– volume: 19
  start-page: 235
  issue: 4
  year: 2013
  ident: 169_CR3
  publication-title: Healthc Inform Res
  doi: 10.4258/hir.2013.19.4.235
– volume: 5
  start-page: 48
  year: 2014
  ident: 169_CR43
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-5-48
– ident: 169_CR36
– volume: 1
  start-page: 33
  issue: 1, 2
  year: 2010
  ident: 169_CR62
  publication-title: Semantic Web
  doi: 10.3233/SW-2010-0014
– volume: 1060
  start-page: 62
  year: 2013
  ident: 169_CR37
  publication-title: 4th Int Confer Biomed Ontol (ICBO-2013)
– volume: 25
  start-page: 25
  issue: 1
  year: 2000
  ident: 169_CR8
  publication-title: Nat Genet
  doi: 10.1038/75556
– volume: 3
  start-page: 160018
  year: 2016
  ident: 169_CR27
  publication-title: Sci Data
  doi: 10.1038/sdata.2016.18
– volume: 28
  start-page: 935
  issue: 9
  year: 2010
  ident: 169_CR6
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt.1666
– volume: 29
  start-page: 525
  issue: 4
  year: 2013
  ident: 169_CR35
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts718
– volume-title: M2: a language for mapping spreadsheets to OWL
  year: 2010
  ident: 169_CR42
– volume: 7
  start-page: 36
  year: 2014
  ident: 169_CR57
  publication-title: BioData Mining
  doi: 10.1186/s13040-014-0036-y
– ident: 169_CR26
– ident: 169_CR22
– ident: 169_CR4
  doi: 10.1093/bib/bbv011
– volume: 12
  start-page: e1004743
  issue: 2
  year: 2016
  ident: 169_CR28
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1004743
– volume: 30
  start-page: 1340
  issue: 9
  year: 2014
  ident: 169_CR19
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu008
– volume: 27
  start-page: 797
  issue: 6
  year: 2011
  ident: 169_CR64
  publication-title: Futur Gener Comput Syst
  doi: 10.1016/j.future.2010.10.011
– volume: 45
  start-page: D347
  issue: D1
  year: 2017
  ident: 169_CR21
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkw918
– volume: 11
  start-page: e0154556
  issue: 4
  year: 2016
  ident: 169_CR7
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0154556
– volume: 14
  start-page: 696
  issue: 6
  year: 2013
  ident: 169_CR29
  publication-title: Brief Bioinform
  doi: 10.1093/bib/bbs053
– volume: 6
  start-page: 23
  year: 2011
  ident: 169_CR30
  publication-title: Appl Ontol
  doi: 10.3233/AO-2011-0087
– ident: 169_CR32
– volume: 3
  start-page: 17
  issue: 1
  year: 2012
  ident: 169_CR51
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-3-17
– volume: 7
  start-page: 18
  year: 2016
  ident: 169_CR59
  publication-title: J Biomed Semantics
  doi: 10.1186/s13326-016-0060-6
– ident: 169_CR50
  doi: 10.1038/npre.2009.3553
– volume: 4
  start-page: S6
  issue: Suppl 1
  year: 2013
  ident: 169_CR55
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-4-S1-S6
– volume: 39
  start-page: W541
  issue: Web Server issu
  year: 2011
  ident: 169_CR2
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkr469
– volume: 16
  start-page: 126
  year: 2015
  ident: 169_CR61
  publication-title: BMC Bioinformatics
  doi: 10.1186/s12859-015-0559-3
– volume: 5
  start-page: S5
  issue: Suppl 1 Proceed
  year: 2014
  ident: 169_CR60
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-5-S1-S5
– volume: 7
  start-page: 53
  issue: 1
  year: 2016
  ident: 169_CR49
  publication-title: J Biomed Semantics
  doi: 10.1186/s13326-016-0100-2
– volume-title: Building Ontologies using basic formal ontology
  year: 2015
  ident: 169_CR33
  doi: 10.7551/mitpress/9780262527811.001.0001
– ident: 169_CR23
– volume: 7
  start-page: 29
  year: 2016
  ident: 169_CR14
  publication-title: J Biomed Semantics
  doi: 10.1186/s13326-016-0069-x
– volume: 7
  start-page: 17
  year: 2016
  ident: 169_CR45
  publication-title: J Biomed Semantics
  doi: 10.1186/s13326-016-0055-3
– volume: 25
  start-page: 1251
  issue: 11
  year: 2007
  ident: 169_CR1
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt1346
– volume: 6
  start-page: 4
  issue: 1
  year: 2015
  ident: 169_CR20
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-6-4
– ident: 169_CR52
– volume: 33
  start-page: W783
  issue: Web Server issu
  year: 2005
  ident: 169_CR9
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gki470
– volume: 2
  start-page: 113
  issue: 3
  year: 2016
  ident: 169_CR15
  publication-title: Curr Pharmacol Rep
  doi: 10.1007/s40495-016-0055-0
– ident: 169_CR34
– volume: 2011
  start-page: bar045
  year: 2011
  ident: 169_CR16
  publication-title: Database
  doi: 10.1093/database/bar045
– ident: 169_CR63
  doi: 10.1007/978-3-642-22630-4_6
– volume: 5
  start-page: 29
  year: 2014
  ident: 169_CR40
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-5-29
– volume: 13
  start-page: S5
  issue: Suppl 1
  year: 2012
  ident: 169_CR44
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-13-S1-S5
– volume: 59
  start-page: 35
  issue: 9
  year: 2016
  ident: 169_CR65
  publication-title: Commun ACM
  doi: 10.1145/2890489
– volume: 4
  start-page: 40
  issue: 1
  year: 2013
  ident: 169_CR5
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-4-40
– volume: 5
  start-page: 1
  issue: 3
  year: 2009
  ident: 169_CR25
  publication-title: Int J Semantic Web Inform Syst
  doi: 10.4018/jswis.2009081901
– volume: 4
  start-page: 33
  issue: 1
  year: 2013
  ident: 169_CR58
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-4-33
– volume: 38
  start-page: W155
  issue: Web Server issu
  year: 2010
  ident: 169_CR47
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkq331
– volume: 2
  start-page: S1
  issue: Suppl 5
  year: 2011
  ident: 169_CR39
  publication-title: J Biomed Semantics
  doi: 10.1186/2041-1480-2-S5-S1
– volume: 18
  start-page: 1
  issue: 1
  year: 2003
  ident: 169_CR31
  publication-title: Knowl Eng Rev
  doi: 10.1017/S0269888903000651
– volume: 2010
  start-page: 856842
  year: 2010
  ident: 169_CR56
  publication-title: J Biomed Biotechnol
SSID ssj0000331083
Score 2.3883548
SecondaryResourceType review_article
Snippet Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed,...
Abstract Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies...
SourceID doaj
pubmedcentral
proquest
gale
pubmed
crossref
springer
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 3
SubjectTerms Algorithms
Analysis
Bioinformatics
Biological Ontologies
Combinatorial Libraries
Computational Biology/Bioinformatics
Computational linguistics
Computer Appl. in Life Sciences
Data Mining and Knowledge Discovery
eXtensible ontology development
Interoperability
Language processing
Mathematics
Mathematics and Statistics
Natural language interfaces
Ontoanimal tools
Ontofox
Ontology
Review
Semantics
Software
SummonAdditionalLinks – databaseName: DOAJ Directory of Open Access Journals
  dbid: DOA
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwELZQT1wQz7JQkJEQT0VN_EjiY3lUFSpwodLeLD_GotI2uzS7B_49M3lsN0XAhVOk2E6cmbHnG3vymbHnSWuHSNTg-JY-U4WPmYNSZQ7dq0xVYYKin5M_fylPztSnuZ7vHPVFOWE9PXAvuEOTQoRK6iKCU1qqWkGdUtRCByW8TDT7os_bCaa6OVgibKnlsI1Z1OVhi8GYoOCZMi2xb2LiiDq-_t9n5R23dD1l8tq-aeeOjm-zWwOO5Ed9_--wG9DcZfunw-pjy1_w0y1hcnuP_UBz4DDv0tX9AjixFtB6Oo9XSUP81fzrh9d8NS6_t9w1ka-XywU_vxjTzEmPeI-3mxUh96sHEe8ELexf9sTfP--zs-OP396fZMNpC1lAyLbOknCAIqoTOnyAFKUTwgehQh4C7frmJvncB1OCcAIvBTjppQDngnZKGfmA7TXLBh4yLn2FsMREqZxRLggT6jwgMoxVLBJEPWP5KHobBipyOhFjYbuQpC5try2L2rKkLStm7M22yarn4fhb5Xekz21FotDubqBh2cGw7L8Ma8ZekjVYGujYueCG_xXwE4kyyx5pIl-UlcLXHUxq4gANk-Jnoz1ZKqKstgaWm9ZSvhrGe4hQZ2y_t69tnxGGCaMNtq4mljf5qGlJc_694wfHRyJIx5ZvRxu1w8TU_llmj_6HzB6zmwgoKTsyK8QB21tfbuAJgra1f9qNz1_JL0Bb
  priority: 102
  providerName: Directory of Open Access Journals
– databaseName: Springer Nature Open Access Journals
  dbid: C6C
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwELZQucABQYGytCAjIZ6KSPxI4mMpVBVq4UKlvVl-qpWW7LbZPfDvmUmctCkPidNK8WOTzIzn88z4CyEvo5QGkKgC--Y2E4X1mQmlyAy4Vx6rQjmBh5NPvpZHp-LLXM4TWTSehbmevy_q8kMLeyiGe14skIQpYbW9LZFmDPOy5cEYTsk54JSap7zlH0dOPE9H0P_7MnzND92skbyRKO38z-F9ci8BR7rfS_oBuRWabbJznMKNLX1Fj0eG5Hab3D0Z-Vjbh-QCtIGGeVetbheBImkBhtOpv6oZom_m3z69pash-t5S03i6Xi4X9PzHUGWOYoRrtN2sELhfTYS0ExjXv-x5v38-IqeHn78fHGXpYwuZA8S2ziIzAV5YHcHfhxA9N4xZx4TLncOkb66iza1TZWCGwU8RDLecBWOcNEIo_phsNcsmPCGU2wpQifJcGCWMY8rVuQNg6CtfxODljOSDILRLTOT4QYyF7nYkdal72WmQnUbZaTYj78Yhq56G41-dP6J0x47IoN1dAMXSySC1is6HisvCByMkF7UIdYxeMukEszzOyGvUDY12DjfnTDquAI-IjFl6XyL3Iq8E_N3epCfYp5s0vxi0S2MTFrU1YblpNZarwXYPAOqM7PTaNt4zoDCmpILR1UQPJw81bWnOzzp6cJgSMDqMfD9orE7rUvv3d_b0v3rvkjsAHLEKMivYHtlaX27CMwBna_u8M8tf7Wkz7A
  priority: 102
  providerName: Springer Nature
Title The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
URI https://link.springer.com/article/10.1186/s13326-017-0169-2
https://www.ncbi.nlm.nih.gov/pubmed/29329592
https://www.proquest.com/docview/1989576929
https://pubmed.ncbi.nlm.nih.gov/PMC5765662
https://doaj.org/article/9fcde7351dea453484e8ffd525c42b3f
Volume 9
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Zb9NAEF6V9oUXxFkCJVokxCmDvYePB4TS0FBFbUFAJL-t1ntApeCkcSLRf8-MY6e4FCRebGkv27Mzu9_sjr8l5ImXUgMSzcC-eRGIqLCBdrEINEyv3CdRZgT-nHx8Eh9OxDiX-RZpj7dqBFhd6drheVKTxfT1z7Pzd2Dwb2uDT-M3FfhZDP1iDKKEx8KIvAMTU4xKftyg_Xpg5oBlamJOFoooAEeg3ee8spXOTFUT-v85bP82b12Oqby0sVrPV6Ob5EYDNOlgrRm3yJYrb5Pdo2Z5sqJP6dGGUbm6Q85AX6jL63j2Yuoo0hrggju1F1FF9Hn-8f0LOm_X5yuqS0uXs9mUnv5o49CxoyGNVqs5SvWiISSmwJX_xZoZ_PwumYwOvg4Pg-Y4hsAAplsGnmkHIko9IALnvOWascIwYUJjcFs4zHwRFiaLHdMMbpHTvODMaW2kFiLj98h2OSvdfUJ5kQBuySwXOhPasMykoQHoaBMbeWdlj4St6JVpuMrxyIypqn2WNFbr3lLQWwp7S7EeebmpMl8Tdfyr8D7256YgcmzXCbPFN9WYrMq8sS7hMrJOC8lFKlzqvZVMGsEK7nvkGWqDQt2ElzO6-aEBPhE5tdRAIjsjTwQ8bq9TEizYdLIft_qkMAvD3ko3W1UKA9rAIQQI2yO7a_3avDPgNJbJDGonHc3rfFQ3pzz9XhOIQ5OA4qHmq1ZHVWt4f5fZg_8R8ENyHZAlhkkGEdsj28vFyj0C9LYs-uRakidwTUcf-mRnMBh_GcN9_-Dk02dIHcbDfr0u0q9t9xfJxkYS
linkProvider Scholars Portal
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Jb9NAFB6hcgAOCAqUlAKDhNgqC3sW23MshSpAUi6tlNtoVlEpdUKdHPj3vGc7bl0WiVMkzxLb772Z7y3zmZCXUUoDSFSBfXObiMz6xIRcJAa2Vx6LTDmBh5Onx_n4VHyZyVlHFo1nYa7m77Myf1-DD8XQ58UCSZgSVtubAhzlJi-bH_bhlJQDTil5l7f848jBztMQ9P--DF_Zh67XSF5LlDb7z9E9crcDjvSglfR9ciNU22Rn0oUba_qKTnqG5Hqb3Jn2fKz1A_IDtIGGWVOtbueBImkBhtOpv6wZom9m3z6-pctN9L2mpvJ0tVjM6dn5psocxQjXaL1eInC_nAhpJzCuf9Hyfv98SE6PPp0cjpPuYwuJA8S2SiIzAV5YGWG_DyF6bhizjgmXOodJ31RFm1qn8sAMg58sGG45C8Y4aYRQ_BHZqhZVeEwotwWgEuW5MEoYx5QrUwfA0Bc-i8HLEUk3gtCuYyLHD2LMdeORlLluZadBdhplp9mIvOuHLFsajn91_oDS7Tsig3ZzARRLdwapVXQ-FFxmPhghuShFKGP0kkknmOVxRF6jbmi0c7g5Z7rjCvCIyJilDyRyL_JCwN_tDXqCfbpB84uNdmlswqK2KizWtcZyNXD3AKCOyE6rbf09AwpjSioYXQz0cPBQw5bq7HtDDw5TAkaHkfsbjdXdulT__Z3t_lfv5-TW-GQ60ZPPx1-fkNsAIrEiMsnYHtlaXazDUwBqK_usMdFfigw22Q
linkToPdf http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Zb9QwELbQVkLwgKBAWShgJMRVRU185HhcKKuybAsSVNo3y_EBlZbsssk-8O-ZyVVSDomnSL7iZGbsz-PxZ0Keeik1INEM7JvngYhyG2gXi0DD9Mp9EmVG4OHkk9P4-EzMFnLR3nNadtHu3ZZkc6YBWZqK6nBtfWPiaXxYwsqK4UoYwybhRTAG76QxoIcR2ZlMZp9mvZsl5IBfUt7uZ_6x7mBGqon7fx-ef5mfLsdOXtpAreel6U1yowWUdNJowC1yxRW7ZG_euiFL-ozOe-bkcpdcP-l5Wsvb5DtoCXWLOoo9XzqKZAboZqf2IpaIvlh8OHpJ151XvqS6sLRarZb0_FsXfY7ihTRabtcI6C8aQjoK9PdvGj7wH3fI2fTt5zfHQXsJQ2AAyVWBZ9rBD0s94ADnvOWasdwwYUJjcDM4zHwe5iaLHdMMHpHTPOfMaW2kFiLjd8moWBXuHqE8TwCtZJYLnQltWGbS0ABgtImNvLNyTMJOEMq0DOV4UcZS1SuVNFaN7BTITqHsFBuTV32VdUPP8a_Cr1G6fUFk1q4TVpsvqjVUlXljXcJlZJ0WkotUuNR7K5k0guXcj8lz1A2F9g-dM7o9xgCfiExaaiKRk5EnAl63PygJdmsG2U867VKYhcFuhVttS4VhbLAMBOA6JnuNtvV9BnTGMplB7WSgh4OPGuYU519r2nBoErA71DzoNFa141X59392_79KPyZXPx5N1fzd6fsH5BpgSwyUDCK2T0bVZuseAn6r8ketjf4EXdtAhw
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The+eXtensible+ontology+development+%28XOD%29+principles+and+tool+implementation+to+support+ontology+interoperability&rft.jtitle=Journal+of+biomedical+semantics&rft.au=He%2C+Yongqun&rft.au=Xiang%2C+Zuoshuang&rft.au=Zheng%2C+Jie&rft.au=Lin%2C+Yu&rft.date=2018-01-12&rft.issn=2041-1480&rft.eissn=2041-1480&rft.volume=9&rft.issue=1&rft_id=info:doi/10.1186%2Fs13326-017-0169-2&rft.externalDBID=n%2Fa&rft.externalDocID=10_1186_s13326_017_0169_2
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2041-1480&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2041-1480&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2041-1480&client=summon