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The '''Open Biological and Biomedical Ontologies''' ('''OBO''') '''Foundry''' is a group of people dedicated to build and maintain [[Ontology (information science)|ontologies]] related to the [[List of life sciences|life sciences]],<ref name=":0">{{cite journal | vauthors = Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S | display-authors = 6 | title = The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration | journal = Nature Biotechnology | volume = 25 | issue = 11 | pages = 1251–5 | date = November 2007 | pmid = 17989687 | pmc = 2814061 | doi = 10.1038/nbt1346 }}</ref> and it is behind the [[OBO_Foundry#Open_Biological_and_Biomedical_Ontologies|Open Biomedical Ontologies]] effort. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable [[reference ontologies]] in the biomedical domain. Currently, there are more than a hundred [[List of OBO Foundry ontologies|ontologies that follow the OBO Foundry principles]].
The '''Open Biological and Biomedical Ontologies''' ('''OBO''') '''Foundry''' is a group of people dedicated to build and maintain [[Ontology (information science)|ontologies]] related to the [[List of life sciences|life sciences]].<ref name=":0">{{cite journal | vauthors = Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S | display-authors = 6 | title = The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration | journal = Nature Biotechnology | volume = 25 | issue = 11 | pages = 1251–5 | date = November 2007 | pmid = 17989687 | pmc = 2814061 | doi = 10.1038/nbt1346 }}</ref> The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable [[reference ontologies]] in the biomedical domain. Currently, there are more than a hundred [[List of OBO Foundry ontologies|ontologies that follow the OBO Foundry principles]].


The OBO Foundry effort makes it easier to integrate biomedical results. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a [[phenotype]] in a [[mouse model]] and its related phenotype in [[zebrafish]]).<ref>{{Cite journal|last=Mungall|first=Christopher J|last2=Gkoutos|first2=Georgios V|last3=Smith|first3=Cynthia L|last4=Haendel|first4=Melissa A|last5=Lewis|first5=Suzanna E|last6=Ashburner|first6=Michael|date=2010|title=Integrating phenotype ontologies across multiple species|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847714/|journal=Genome Biology|volume=11|issue=1|pages=R2|doi=10.1186/gb-2010-11-1-r2|issn=1465-6906|pmc=2847714|pmid=20064205}}</ref>
The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in [[bioinformatics]]. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a [[phenotype]] in a [[mouse model]] and its related phenotype in [[zebrafish]]).<ref>{{Cite journal|last1=Mungall|first1=Christopher J|last2=Gkoutos|first2=Georgios V|last3=Smith|first3=Cynthia L|last4=Haendel|first4=Melissa A|author-link4=Melissa Haendel |last5=Lewis|first5=Suzanna E|last6=Ashburner|first6=Michael|date=2010|title=Integrating phenotype ontologies across multiple species|journal=Genome Biology|volume=11|issue=1|pages=R2|doi=10.1186/gb-2010-11-1-r2|issn=1465-6906|pmc=2847714|pmid=20064205 |doi-access=free }}</ref>


== Introduction ==
== Introduction ==
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The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using [[Controlled vocabulary|controlled vocabularies]]. Ideally, such controlled vocabularies take the form of [[Ontology (information science)|ontologies]], which support logical reasoning over the data annotated using the terms in the vocabulary.
The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using [[Controlled vocabulary|controlled vocabularies]]. Ideally, such controlled vocabularies take the form of [[Ontology (information science)|ontologies]], which support logical reasoning over the data annotated using the terms in the vocabulary.


The formalization of concepts in the biomedical domain is especially known via the work of the [[Gene Ontology]] Consortium, a part of the OBO Foundry. This has led to the development of certain proposed principles of good practice in ontology development, which are now being put into practice within the framework of the [[Open Biomedical Ontologies]] consortium through its OBO Foundry initiative. OBO ontologies form part of the resources of the [[National Center for Biomedical Ontology]], where they form a central component of the NCBO's BioPortal.
The formalization of concepts in the biomedical domain is especially known via the work of the [[Gene Ontology]] Consortium, a part of the OBO Foundry. This has led to the development of certain proposed principles of good practice in ontology development, which are now being put into practice within the framework of the Open Biomedical Ontologies consortium through its OBO Foundry initiative. OBO ontologies form part of the resources of the [[National Center for Biomedical Ontology]], where they form a central component of the NCBO's BioPortal.


== Open Biological and Biomedical Ontologies ==
== Open Biological and Biomedical Ontologies ==
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A subset of the original OBO ontologies has started the OBO Foundry, which leads the OBO efforts since 2007.<ref name=":0" />
A subset of the original OBO ontologies has started the OBO Foundry, which leads the OBO efforts since 2007.<ref name=":0" />


The creation of OBO in 2001 was largely inspired by the efforts of the [[Gene ontology|Gene Ontology]] project.<ref>{{Cite journal|last=Shimoyama|first=Mary|last2=Shimoyama|first2=Mary|last3=Dwinell|first3=Melinda|last4=Jacob|first4=Howard|date=2009-08-05|title=Multiple Ontologies for Integrating Complex Phenotype Datasets|url=http://dx.doi.org/10.1038/npre.2009.3554|journal=Nature Precedings|doi=10.1038/npre.2009.3554|issn=1756-0357}}</ref> OBO forms part of the resources of the [[United States|U.S.]] [[National Center for Biomedical Ontology]] (NCBIO) and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.
The creation of OBO in 2001 was largely inspired by the efforts of the [[Gene ontology|Gene Ontology]] project.<ref>{{Cite journal|last1=Shimoyama|first1=Mary|last2=Dwinell|first2=Melinda|last3=Jacob|first3=Howard|date=2009-08-05|title=Multiple Ontologies for Integrating Complex Phenotype Datasets|journal=Nature Precedings|doi=10.1038/npre.2009.3554|issn=1756-0357|doi-access=free}}</ref> OBO forms part of the resources of the [[United States|U.S.]] [[National Center for Biomedical Ontology]] (NCBIO) and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.


== Rules for participation ==
== Rules for participation ==


The OBO Foundry is open to participations of any interested individuals. Ontologies that intend to be officially part of the OBO Foundry have to adhere to the OBO principles and pass a series of reviews done by the members, when "the Foundry coordinators serve as analogs of journal editors".<ref name=":0" /> There are ontologies that follow OBO principles but are not officially part of OBO, such as [[eagle-i]]'s Reagent Application Ontology.<ref>{{cite journal |last=Brush |first=Matthew H. |last2=Vasilevsky |first2=Nicole |last3=Torniai |first3=Carlo |last4=Johnson |first4=Tenille |last5=Shaffer |first5=Christopher |last6=Haendel |first6=Melissa | name-list-format = vanc |date=2011|title=Developing a reagent application ontology within the OBO foundry framework |url= https://ohsu.pure.elsevier.com/en/publications/developing-a-reagent-application-ontology-within-the-obo-foundry--2 |journal=CEUR Workshop Proceedings |pages=234–236 }}</ref> and the Animals in Context Ontology.<ref>{{cite conference | vauthors = Santamaria SL | url = http://kr-med.org/icbofois2012/proceedings/ICBO2012/ICBO2012PapersSingleFiles/ICBO-2012-session1-paper04-santamaria.pdf | title = Development the Animals in Context ontology | conference = Proceedings of the International Conference on Biomedical Ontology | location = Graz | date = 2012 }}</ref>
The OBO Foundry is open to participations of any interested individuals. Ontologies that intend to be officially part of the OBO Foundry have to adhere to the OBO principles and pass a series of reviews done by the members, when "the Foundry coordinators serve as analogs of journal editors".<ref name=":0" /> There are ontologies that follow OBO principles but are not officially part of OBO, such as [[eagle-i]]'s Reagent Application Ontology.<ref>{{cite journal |last1=Brush |first1=Matthew H. |last2=Vasilevsky |first2=Nicole |last3=Torniai |first3=Carlo |last4=Johnson |first4=Tenille |last5=Shaffer |first5=Christopher |last6=Haendel |first6=Melissa | name-list-style = vanc |date=2011|title=Developing a reagent application ontology within the OBO foundry framework |url= https://ohsu.pure.elsevier.com/en/publications/developing-a-reagent-application-ontology-within-the-obo-foundry--2 |journal=CEUR Workshop Proceedings |volume=833 |pages=234–236 }}</ref> and the Animals in Context Ontology.<ref>{{cite conference | vauthors = Santamaria SL | url = http://kr-med.org/icbofois2012/proceedings/ICBO2012/ICBO2012PapersSingleFiles/ICBO-2012-session1-paper04-santamaria.pdf | title = Development the Animals in Context ontology | conference = Proceedings of the International Conference on Biomedical Ontology | location = Graz | date = 2012 }}</ref>


An integration into OBO of the [[OntoClean|OntoClean's theory of rigidity]] has been proposed as a step to standardize candidate ontologies. This integration would make it easier to develop software to automatically check candidates.<ref>{{Cite conference|last=Seyed, Patrice, and Stuart C. Shapiro.|first=|date=2011|title=Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies|url=http://ceur-ws.org/Vol-833/paper23.pdf|conference=Proceedings of the International Conference on Biomedical Ontology (CEUR 993)|volume=|pages=|via=}}</ref>
An integration into OBO of the [[OntoClean|OntoClean's theory of rigidity]] has been proposed as a step to standardize candidate ontologies. This integration would make it easier to develop software to automatically check candidates.<ref>{{Cite conference|last=Seyed, Patrice, and Stuart C. Shapiro.|date=2011|title=Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies|url=http://ceur-ws.org/Vol-833/paper23.pdf|conference=Proceedings of the International Conference on Biomedical Ontology (CEUR 993)}}</ref>


== Tools ==
== Tools ==
The OBO Foundry community is also dedicated to develop tools to facilitate creating and maintaining ontologies. Most ontology developers in OBO use the [[Protégé (software)|Protégé]] ontology editor and the [[Web Ontology Language]] (OWL) for building ontologies. To facilitate [[Command-line interface|command line]] management of ontologies in a Protégé- and OWL-compatible format, the OBO Foundry has developed the tool ROBOT (ROBOT is and OBO Tool). ROBOT aggregates functions for routine tasks in ontology development, is [[Open-source software|open source]], and can be used either via the command line or as a library for any language on the [[Java virtual machine|Java Virtual Machine]].<ref>{{cite journal | vauthors = Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA | title = ROBOT: A Tool for Automating Ontology Workflows | journal = BMC Bioinformatics | volume = 20 | issue = 1 | pages = 407 | date = July 2019 | pmid = 31357927 | pmc = 6664714 | doi = 10.1186/s12859-019-3002-3 }}</ref>
The OBO Foundry community is also dedicated to developing tools to facilitate creating and maintaining ontologies. Most ontology developers in OBO use the [[Protégé (software)|Protégé]] ontology editor and the [[Web Ontology Language]] (OWL) for building ontologies. To facilitate [[Command-line interface|command line]] management of ontologies in a Protégé- and OWL-compatible format, the OBO Foundry has developed the tool ROBOT (ROBOT is an OBO Tool). ROBOT aggregates functions for routine tasks in ontology development, is [[Open-source software|open source]], and can be used either via the command line or as a library for any language on the [[Java virtual machine|Java Virtual Machine]].<ref>{{cite journal | vauthors = Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA | title = ROBOT: A Tool for Automating Ontology Workflows | journal = BMC Bioinformatics | volume = 20 | issue = 1 | pages = 407 | date = July 2019 | pmid = 31357927 | pmc = 6664714 | doi = 10.1186/s12859-019-3002-3 | doi-access = free }}</ref>


Other tool related to the OBO effort is [[Gene ontology#Tools|OBO-Edit]],<ref>{{cite journal | vauthors = Day-Richter J, Harris MA, Haendel M, Lewis S | title = OBO-Edit--an ontology editor for biologists | journal = Bioinformatics | volume = 23 | issue = 16 | pages = 2198–200 | date = August 2007 | pmid = 17545183 | doi = 10.1093/bioinformatics/btm112 | doi-access = free }}</ref> an ontology editor and [[Semantic reasoner|reasoner]] funded by the [[Gene Ontology Consortium]]. There are also plugins for OBO-Edit which facilitate the development of ontologies, such as the semi-automatic ontology generator DOG4DAG.<ref>{{cite journal | vauthors = Wächter T, Schroeder M | title = Semi-automated ontology generation within OBO-Edit | journal = Bioinformatics | volume = 26 | issue = 12 | pages = i88-96 | date = June 2010 | pmid = 20529942 | doi = 10.1093/bioinformatics/btq188 | doi-access = free }}</ref>
Other tool related to the OBO effort is [[Gene ontology#Tools|OBO-Edit]],<ref>{{cite journal | vauthors = Day-Richter J, Harris MA, Haendel M, Lewis S | title = OBO-Edit--an ontology editor for biologists | journal = Bioinformatics | volume = 23 | issue = 16 | pages = 2198–200 | date = August 2007 | pmid = 17545183 | doi = 10.1093/bioinformatics/btm112 | doi-access = free }}</ref> an ontology editor and [[Semantic reasoner|reasoner]] funded by the [[Gene Ontology Consortium]]. There are also plugins for OBO-Edit which facilitate the development of ontologies, such as the semi-automatic ontology generator DOG4DAG.<ref>{{cite journal | vauthors = Wächter T, Schroeder M | title = Semi-automated ontology generation within OBO-Edit | journal = Bioinformatics | volume = 26 | issue = 12 | pages = i88-96 | date = June 2010 | pmid = 20529942 | doi = 10.1093/bioinformatics/btq188 | pmc = 2881373 | doi-access = free }}</ref>


==The OBO file format==
==The OBO file format==
The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of [[Web Ontology Language|Web Ontology Language (OWL)]].
The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of [[Web Ontology Language|Web Ontology Language (OWL)]].


As a community effort, a standard common mapping has been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL.<ref>{{Citation|last=Golbreich|first=Christine|title=OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences|date=2007|url=http://dx.doi.org/10.1007/978-3-540-76298-0_13|work=The Semantic Web|pages=169–182|publisher=Springer Berlin Heidelberg|isbn=978-3-540-76297-3|access-date=2020-03-17|last2=Horridge|first2=Matthew|last3=Horrocks|first3=Ian|last4=Motik|first4=Boris|last5=Shearer|first5=Rob}}</ref> The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.<ref name="pmid18245124">{{Cite journal|last1=Antezana|first1=E.|last2=Egana|first2=M.|last3=De Baets|first3=B.|last4=Kuiper|first4=M.|last5=Mironov|first5=V.|year=2008|title=ONTO-PERL: An API for supporting the development and analysis of bio-ontologies|journal=Bioinformatics|volume=24|issue=6|pages=885–887|doi=10.1093/bioinformatics/btn042|pmc=|pmid=18245124|doi-access=free}}</ref>
As a community effort, standard common mappings have been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL.<ref name=":3">{{Cite journal|last1=Tirmizi|first1=Syed|last2=Aitken|first2=Stuart|last3=Moreira|first3=Dilvan A|last4=Mungall|first4=Chris|last5=Sequeda|first5=Juan|last6=Shah|first6=Nigam H|last7=Miranker|first7=Daniel P|date=2011|title=Mapping between the OBO and OWL ontology languages|journal=Journal of Biomedical Semantics|volume=2|issue=Suppl 1|pages=S3|doi=10.1186/2041-1480-2-s1-s3|pmid=21388572|pmc=3105495|issn=2041-1480 |doi-access=free }}</ref><ref>{{Citation|last1=Golbreich|first1=Christine|title=OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences|date=2007|work=The Semantic Web|pages=169–182|publisher=Springer Berlin Heidelberg|isbn=978-3-540-76297-3|last2=Horridge|first2=Matthew|last3=Horrocks|first3=Ian|last4=Motik|first4=Boris|last5=Shearer|first5=Rob|series=Lecture Notes in Computer Science |volume=4825|doi=10.1007/978-3-540-76298-0_13|bibcode=2007LNCS.4825..169G|doi-access=free}}</ref> The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.<ref name="pmid18245124">{{Cite journal|last1=Antezana|first1=E.|last2=Egana|first2=M.|last3=De Baets|first3=B.|last4=Kuiper|first4=M.|last5=Mironov|first5=V.|year=2008|title=ONTO-PERL: An API for supporting the development and analysis of bio-ontologies|journal=Bioinformatics|volume=24|issue=6|pages=885–887|doi=10.1093/bioinformatics/btn042|pmid=18245124|doi-access=free}}</ref>


== OBO Foundry Ontologies ==
== OBO Foundry Ontologies ==
The initial set of OBO Foundry ontologies was composed by mature ontologies (such as the [[Gene ontology|Gene Ontology]], GO, and the [[Foundational Model of Anatomy]], FMAO), by mergers of previously existing ontologies (ex: the Cell Ontology,<ref>{{Cite journal|last=Diehl|first=Alexander D.|last2=Meehan|first2=Terrence F.|last3=Bradford|first3=Yvonne M.|last4=Brush|first4=Matthew H.|last5=Dahdul|first5=Wasila M.|last6=Dougall|first6=David S.|last7=He|first7=Yongqun|last8=Osumi-Sutherland|first8=David|last9=Ruttenberg|first9=Alan|last10=Sarntivijai|first10=Sirarat|last11=Van Slyke|first11=Ceri E.|date=2016-07-04|title=The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability|url=https://doi.org/10.1186/s13326-016-0088-7|journal=Journal of Biomedical Semantics|volume=7|issue=1|pages=44|doi=10.1186/s13326-016-0088-7|issn=2041-1480|pmc=4932724|pmid=27377652}}</ref> CL, formed from different dedicated ontologies,<ref>{{Cite journal|last=Bard|first=Jonathan|last2=Rhee|first2=Seung Y.|last3=Ashburner|first3=Michael|date=2005-01-14|title=An ontology for cell types|url=https://doi.org/10.1186/gb-2005-6-2-r21|journal=Genome Biology|volume=6|issue=2|pages=R21|doi=10.1186/gb-2005-6-2-r21|issn=1474-760X|pmc=551541|pmid=15693950}}</ref><ref>{{Cite journal|last=Kelso|first=J.|date=2003-05-12|title=eVOC: A Controlled Vocabulary for Unifying Gene Expression Data|url=http://dx.doi.org/10.1101/gr.985203|journal=Genome Research|volume=13|issue=6|pages=1222–1230|doi=10.1101/gr.985203|issn=1088-9051}}</ref> and related parts on GO and FMAO) and by development of new ontologies based on its principles.<ref name=":2">{{Cite journal|last=Smith|first=Barry|last2=Ashburner|first2=Michael|last3=Rosse|first3=Cornelius|last4=Bard|first4=Jonathan|last5=Bug|first5=William|last6=Ceusters|first6=Werner|last7=Goldberg|first7=Louis J|last8=Eilbeck|first8=Karen|last9=Ireland|first9=Amelia|last10=Mungall|first10=Christopher J|last11=Leontis|first11=Neocles|date=November 2007|title=The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration|url=http://dx.doi.org/10.1038/nbt1346|journal=Nature Biotechnology|volume=25|issue=11|pages=1251–1255|doi=10.1038/nbt1346|issn=1087-0156}}</ref>
The initial set of OBO Foundry ontologies was composed by mature ontologies (such as the [[Gene ontology|Gene Ontology]], GO, and the [[Foundational Model of Anatomy]], FMAO), by mergers of previously existing ontologies (ex: the Cell Ontology,<ref>{{Cite journal|last1=Diehl|first1=Alexander D.|last2=Meehan|first2=Terrence F.|last3=Bradford|first3=Yvonne M.|last4=Brush|first4=Matthew H.|last5=Dahdul|first5=Wasila M.|last6=Dougall|first6=David S.|last7=He|first7=Yongqun|last8=Osumi-Sutherland|first8=David|last9=Ruttenberg|first9=Alan|last10=Sarntivijai|first10=Sirarat|last11=Van Slyke|first11=Ceri E.|date=2016-07-04|title=The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability|journal=Journal of Biomedical Semantics|volume=7|issue=1|pages=44|doi=10.1186/s13326-016-0088-7|issn=2041-1480|pmc=4932724|pmid=27377652 |doi-access=free }}</ref> CL, formed from different dedicated ontologies,<ref>{{Cite journal|last1=Bard|first1=Jonathan|last2=Rhee|first2=Seung Y.|last3=Ashburner|first3=Michael|date=2005-01-14|title=An ontology for cell types|journal=Genome Biology|volume=6|issue=2|pages=R21|doi=10.1186/gb-2005-6-2-r21|issn=1474-760X|pmc=551541|pmid=15693950 |doi-access=free }}</ref><ref>{{Cite journal|last=Kelso|first=J.|date=2003-05-12|title=eVOC: A Controlled Vocabulary for Unifying Gene Expression Data|journal=Genome Research|volume=13|issue=6|pages=1222–1230|doi=10.1101/gr.985203|pmid=12799354|pmc=403650|issn=1088-9051}}</ref> and related parts on GO and FMAO) and by development of new ontologies based on its principles.<ref name=":2">{{Cite journal|last1=Smith|first1=Barry|last2=Ashburner|first2=Michael|last3=Rosse|first3=Cornelius|last4=Bard|first4=Jonathan|last5=Bug|first5=William|last6=Ceusters|first6=Werner|last7=Goldberg|first7=Louis J|last8=Eilbeck|first8=Karen|last9=Ireland|first9=Amelia|last10=Mungall|first10=Christopher J|last11=Leontis|first11=Neocles|date=November 2007|title=The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration|journal=Nature Biotechnology|volume=25|issue=11|pages=1251–1255|doi=10.1038/nbt1346|pmid=17989687|pmc=2814061|issn=1087-0156}}</ref>


The original set of ontologies also included the Zebrafish Anatomical Ontology<ref>{{Cite journal|last=Van Slyke|first=Ceri E.|last2=Bradford|first2=Yvonne M.|last3=Westerfield|first3=Monte|last4=Haendel|first4=Melissa A.|date=2014-02-25|title=The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio|url=https://doi.org/10.1186/2041-1480-5-12|journal=Journal of Biomedical Semantics|volume=5|issue=1|pages=12|doi=10.1186/2041-1480-5-12|issn=2041-1480|pmc=3944782|pmid=24568621}}</ref> (a part of the [[Zebrafish Information Network]]), the [[ChEBI|CheBI]] ontology, the [[Disease Ontology]], the [[Plant ontology|Plant Ontology]], the [[Sequence Ontology]], the [[Ontology for Biomedical Investigations]] and the [[Protein ontology|Protein Ontology]].<ref name=":2" />
The original set of ontologies also included the Zebrafish Anatomical Ontology<ref>{{Cite journal|last1=Van Slyke|first1=Ceri E.|last2=Bradford|first2=Yvonne M.|last3=Westerfield|first3=Monte|last4=Haendel|first4=Melissa A.|date=2014-02-25|title=The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio|journal=Journal of Biomedical Semantics|volume=5|issue=1|pages=12|doi=10.1186/2041-1480-5-12|issn=2041-1480|pmc=3944782|pmid=24568621 |doi-access=free }}</ref> (a part of the [[Zebrafish Information Network]]), the [[ChEBI|CheBI]] ontology, the [[Disease Ontology]], the [[Plant ontology|Plant Ontology]], the [[Sequence Ontology]], the [[Ontology for Biomedical Investigations]] and the [[Protein ontology|Protein Ontology]].<ref name=":2" />


The number of ontologies in OBO has grown to the order of hundreds, and they are gathered in the [[list of OBO Foundry ontologies]].
The number of ontologies in OBO has grown to the order of hundreds, and they are gathered in the [[list of OBO Foundry ontologies]].
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== OBO Foundry and Wikidata ==
== OBO Foundry and Wikidata ==


A number of different OBO Foundry ontologies have also been integrated to the [[Wikidata]] knowledge graph.<ref>{{Cite journal|last=Waagmeester|first=Andra|last2=Stupp|first2=Gregory|last3=Burgstaller-Muehlbacher|first3=Sebastian|last4=Good|first4=Benjamin M|last5=Griffith|first5=Malachi|last6=Griffith|first6=Obi L|last7=Hanspers|first7=Kristina|last8=Hermjakob|first8=Henning|last9=Hudson|first9=Toby S|last10=Hybiske|first10=Kevin|last11=Keating|first11=Sarah M|date=2020-03-17|editor-last=Rodgers|editor-first=Peter|editor2-last=Mungall|editor2-first=Chris|title=Wikidata as a knowledge graph for the life sciences|url=https://doi.org/10.7554/eLife.52614|journal=eLife|volume=9|pages=e52614|doi=10.7554/eLife.52614|issn=2050-084X}}</ref> This has led to the integration of OBO structured ontologies to data from other, non-OBO databases . For example, the integration of the [[Human Disease Ontology]] <ref>{{Cite journal|last=Schriml|first=Lynn M.|last2=Mitraka|first2=Elvira|last3=Munro|first3=James|last4=Tauber|first4=Becky|last5=Schor|first5=Mike|last6=Nickle|first6=Lance|last7=Felix|first7=Victor|last8=Jeng|first8=Linda|last9=Bearer|first9=Cynthia|last10=Lichenstein|first10=Richard|last11=Bisordi|first11=Katharine|date=2019-01-08|title=Human Disease Ontology 2018 update: classification, content and workflow expansion|url=https://academic.oup.com/nar/article/47/D1/D955/5165342|journal=Nucleic Acids Research|language=en|volume=47|issue=D1|pages=D955–D962|doi=10.1093/nar/gky1032|issn=0305-1048}}</ref> to Wikidata has enabled its link to the description of [[Cell line|cell-lines]] from the resource [[Cellosaurus]].<ref>{{Cite web|title=HeLa|url=https://www.wikidata.org/wiki/Q847482|website=www.wikidata.org|language=en|access-date=2020-05-04}}</ref> One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies. Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise). <ref>{{Cite journal|last=Jacobsen|first=Annika|last2=Waagmeester|first2=Andra|last3=Kaliyaperumal|first3=Rajaram|last4=Stupp|first4=Gregory S.|last5=M. Schriml|first5=Lynn|last6=Thompson|first6=Mark|last7=I. Su|first7=Andrew|last8=Roos|first8=Marco|date=2018-12-04|title=Wikidata as an intuitive resource towards semantic data modeling in data FAIRification|url=https://swat4hcls.figshare.com/articles/Wikidata_as_an_intuitive_resource_towards_semantic_data_modeling_in_data_FAIRification/7415282|language=en|doi=10.6084/m9.figshare.7415282.v2}}</ref>
A number of different OBO Foundry ontologies have also been integrated to the [[Wikidata]] knowledge graph.<ref>{{Cite journal|last1=Waagmeester|first1=Andra|last2=Stupp|first2=Gregory|last3=Burgstaller-Muehlbacher|first3=Sebastian|last4=Good|first4=Benjamin M|last5=Griffith|first5=Malachi|last6=Griffith|first6=Obi L|last7=Hanspers|first7=Kristina|last8=Hermjakob|first8=Henning|last9=Hudson|first9=Toby S|last10=Hybiske|first10=Kevin|last11=Keating|first11=Sarah M|date=2020-03-17|editor-last=Rodgers|editor-first=Peter|editor2-last=Mungall|editor2-first=Chris|title=Wikidata as a knowledge graph for the life sciences|journal=eLife|volume=9|pages=e52614|doi=10.7554/eLife.52614|pmid=32180547|pmc=7077981|issn=2050-084X |doi-access=free }}</ref><ref>{{Cite journal|last1=Turki|first1=Houcemeddine|last2=Shafee|first2=Thomas|last3=Hadj Taieb|first3=Mohamed Ali|last4=Ben Aouicha|first4=Mohamed|last5=Vrandečić|first5=Denny|last6=Das|first6=Diptanshu|last7=Hamdi|first7=Helmi|date=2019-11-01|title=Wikidata: A large-scale collaborative ontological medical database|journal=Journal of Biomedical Informatics|language=en|volume=99|pages=103292|doi=10.1016/j.jbi.2019.103292|pmid=31557529|issn=1532-0464|doi-access=free}}</ref> This has led to the integration of OBO structured ontologies to data from other, non-OBO databases . For example, the integration of the [[Human Disease Ontology]]<ref>{{Cite journal|last1=Schriml|first1=Lynn M.|last2=Mitraka|first2=Elvira|last3=Munro|first3=James|last4=Tauber|first4=Becky|last5=Schor|first5=Mike|last6=Nickle|first6=Lance|last7=Felix|first7=Victor|last8=Jeng|first8=Linda|last9=Bearer|first9=Cynthia|last10=Lichenstein|first10=Richard|last11=Bisordi|first11=Katharine|date=2019-01-08|title=Human Disease Ontology 2018 update: classification, content and workflow expansion|journal=Nucleic Acids Research|language=en|volume=47|issue=D1|pages=D955–D962|doi=10.1093/nar/gky1032|pmid=30407550|pmc=6323977|issn=0305-1048}}</ref> to Wikidata has enabled its link to the description of [[Cell line|cell-lines]] from the resource [[Cellosaurus]].<ref>{{Cite web|title=HeLa|url=https://www.wikidata.org/wiki/Q847482|website=www.wikidata.org|language=en|access-date=2020-05-04}}</ref> One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies. Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise).<ref>{{Cite journal|last1=Jacobsen|first1=Annika|last2=Waagmeester|first2=Andra|last3=Kaliyaperumal|first3=Rajaram|last4=Stupp|first4=Gregory S.|last5=M. Schriml|first5=Lynn|last6=Thompson|first6=Mark|last7=I. Su|first7=Andrew|last8=Roos|first8=Marco|date=2018-12-04|title=Wikidata as an intuitive resource towards semantic data modeling in data FAIRification|journal=Figshare|url=https://swat4hcls.figshare.com/articles/Wikidata_as_an_intuitive_resource_towards_semantic_data_modeling_in_data_FAIRification/7415282|language=en|doi=10.6084/m9.figshare.7415282.v2}}</ref>


== Principles. ==
== Principles ==


Summary of OBO Foundry Principles<ref>{{Cite web|url=http://obofoundry.org/principles/fp-000-summary.html|title=Overview|website=obofoundry.org|access-date=2020-02-06}}</ref> for development of an OBO-compatible life sciences [[ontology]]:
Summary of OBO Foundry Principles<ref>{{Cite web|url=http://obofoundry.org/principles/fp-000-summary.html|title=Overview|website=obofoundry.org|access-date=2020-02-06}}</ref> for development of an OBO-compatible life sciences [[ontology]]:


===== Openess =====
=== Openness ===
The ontologies are openly available and have to be released under either the license [[CC-BY 3.0]] or under the public domain ([[CC0]]).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-001-open.html|title=Open (principle 1)|website=obofoundry.org|access-date=2020-02-06}}</ref> The openess of the ontologies has enabled, for example, the import of terms from the [[Gene Ontology]] (one of the ontologies that follow OBO Principles) to the [[Wikidata]] project.<ref>{{cite journal | vauthors = Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI | display-authors = 6 | title = Wikidata as a semantic framework for the Gene Wiki initiative | journal = Database | volume = 2016 | date = 2016-01-01 | pmid = 26989148 | pmc = 4795929 | doi = 10.1093/database/baw015 | url = https://academic.oup.com/database/article/doi/10.1093/database/baw015/2630183 }}</ref>
The ontologies are openly available and have to be released under either the license [[CC-BY 3.0]] or under the public domain ([[CC0]]).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-001-open.html|title=Open (principle 1)|website=obofoundry.org|access-date=2020-02-06}}</ref> The openness of the ontologies has enabled, for example, the import of terms from the [[Gene Ontology]] (one of the ontologies that follow OBO Principles) to the [[Wikidata]] project.<ref>{{cite journal | vauthors = Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI | display-authors = 6 | title = Wikidata as a semantic framework for the Gene Wiki initiative | journal = Database | volume = 2016 | date = 2016-01-01 | pages = baw015 | pmid = 26989148 | pmc = 4795929 | doi = 10.1093/database/baw015 }}</ref>


===== Common format =====
=== Common format ===
The ontologies have to be available in a common [[formal language]]. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/[[Web Ontology Language|OWL2]] or [[Open Biomedical Ontologies#The OBO file format|OBO]] using a [[RDF/XML]] syntax to maximize interoperability.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-002-format.html|title=Common Format (principle 2)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies have to be available in a common [[formal language]]. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/[[Web Ontology Language|OWL2]] or [[Open Biomedical Ontologies#The OBO file format|OBO]] using a [[RDF/XML]] syntax to maximize interoperability.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-002-format.html|title=Common Format (principle 2)|website=obofoundry.org|access-date=2020-02-06}}</ref>


===== Orthogonality =====
=== Orthogonality ===
[[File:Screenshot_from_2020-05-08_06-52-55.png|thumb|Mapping from OBO IDs to OBO Unified Resource Identifiers (URIs), unique for each item.<ref name=":3" />]]
Terms should be unique in the OBO space, meaning that each item has an unique ontology prefix (such as [[ChEBI|CHEBI]], [[Gene ontology|GO]], [[Protein Information Resource|PRO]]) and a local numeric identifier within the ontology.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-003-uris.html|title=URI/Identifier Space (principle 3)|website=obofoundry.org|access-date=2020-02-06}}</ref> The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.<ref name=":1">{{cite conference |last=Courtot |first=Mélanie |last2=Mungall |first2=Christopher |last3=Brinkman RR |last4=Ruttenberg |first4=Alan | name-list-format = vanc |year=2010|title=Building the OBO Foundry-One Policy at a Time|url=| conference=CEURS Proceedings: International Conference on Biomedical Ontologies|volume=|pages=|via=}}</ref> In order to participate in OBO Foundry, ontologies have to be orthogonal and the concepts it models must be unique within OBO, so each concept has a single [[Universal Resource Identifier]] (URI). New ontologies have, then, to reuse work done in other efforts.<ref name=":1" />
Terms should be unique in the OBO space, meaning that each item has a unique ontology prefix (such as [[ChEBI|CHEBI]], [[Gene ontology|GO]], [[Protein Information Resource|PRO]]) and a local numeric identifier within the ontology.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-003-uris.html|title=URI/Identifier Space (principle 3)|website=obofoundry.org|access-date=2020-02-06}}</ref> The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.<ref name=":1">{{cite conference |last1=Courtot |first1=Mélanie |last2=Mungall |first2=Christopher |last3=Brinkman RR |last4=Ruttenberg |first4=Alan | name-list-style = vanc |year=2010|title=Building the OBO Foundry-One Policy at a Time| conference=CEURS Proceedings: International Conference on Biomedical Ontologies}}</ref> In order to participate in OBO Foundry, ontologies have to be orthogonal and the concepts it models must be unique within OBO, so each concept has a single [[Uniform Resource Identifier]] (URI). New ontologies have, then, to reuse work done in other efforts.<ref name=":1" />


Despite the ideal of uniqueness of terms and interoperability, in practice, this is difficult to enforce, leading to the occurrence of term duplication. Furthermore, some ontologies do not reuse terms or even reuse terms inappropriately.<ref>{{cite journal | vauthors = Ghazvinian A, Noy NF, Musen MA | title = How orthogonal are the OBO Foundry ontologies? | journal = Journal of Biomedical Semantics | volume = 2 Suppl 2 | issue = Suppl 2 | pages = S2 | date = May 2011 | pmid = 21624157 | doi = 10.1186/2041-1480-2-s2-s2 | url = http://dx.doi.org/10.1186/2041-1480-2-s2-s2 | doi-access = free }}</ref>
Despite the ideal of uniqueness of terms and interoperability, in practice, this is difficult to enforce, leading to the occurrence of term duplication. Furthermore, some ontologies do not reuse terms or even reuse terms inappropriately.<ref>{{cite journal | vauthors = Ghazvinian A, Noy NF, Musen MA | title = How orthogonal are the OBO Foundry ontologies? | journal = Journal of Biomedical Semantics | volume = 2 | issue = Suppl 2 | pages = S2 | date = May 2011 | pmid = 21624157 | doi = 10.1186/2041-1480-2-s2-s2 | pmc = 3102891 | doi-access = free }}</ref>


===== Versioning =====
=== Versioning ===
Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains.<ref>{{Cite journal|last=Groß|first=Anika|last2=Pruski|first2=Cédric|last3=Rahm|first3=Erhard|date=2016|title=Evolution of biomedical ontologies and mappings: Overview of recent approaches|url=http://dx.doi.org/10.1016/j.csbj.2016.08.002|journal=Computational and Structural Biotechnology Journal|volume=14|pages=333–340|doi=10.1016/j.csbj.2016.08.002|issn=2001-0370|doi-access=free}}</ref> In order to ensure that new versions are updated, but tools that use older version of the ontologies are still function, OBO enforces a system of [[versioning systems]], with each ontology version receiving an unique identifier, either in the format of a date or a numbering system, and [[metadata]] dags.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-004-versioning.html|title=Versioning (principle 4)|website=obofoundry.org|access-date=2020-02-06}}</ref>
Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains.<ref>{{Cite journal|last1=Groß|first1=Anika|last2=Pruski|first2=Cédric|last3=Rahm|first3=Erhard|date=2016|title=Evolution of biomedical ontologies and mappings: Overview of recent approaches|journal=Computational and Structural Biotechnology Journal|volume=14|pages=333–340|doi=10.1016/j.csbj.2016.08.002|pmid=27642503|pmc=5018063|issn=2001-0370|doi-access=free}}</ref> In order to ensure that new versions are updated, but tools that use older version of the ontologies are still function, OBO enforces a system of [[versioning systems]], with each ontology version receiving a unique identifier, either in the format of a date or a numbering system, and [[metadata]] dags.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-004-versioning.html|title=Versioning (principle 4)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Scope ====
=== Scope ===
The ontologies should have a clearly specified scope (the domain it intends to cover).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-005-delineated-content.html|title=Scope (principle 5)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should have a clearly specified scope (the domain it intends to cover).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-005-delineated-content.html|title=Scope (principle 5)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Have textual definitions ====
=== Have textual definitions ===
The ontologies should have textual definitions for each item, in a [[Human-readable medium|human-readable]] way. That means that beside the alphanumeric identification for each item, they should be described in natural language by logical affirmations following the [[Aristotelian logic]] in a way that is unique within the ontology.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-006-textual-definitions.html|title=Textual Definitions (principle 6)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should have textual definitions for each item, in a [[Human-readable medium|human-readable]] way. That means that beside the alphanumeric identification for each item, they should be described in natural language by logical affirmations following the [[Aristotelian logic]] in a way that is unique within the ontology.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-006-textual-definitions.html|title=Textual Definitions (principle 6)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Standardized relations and the Relation Ontology (RO)====
=== Standardized relations and the Relation Ontology (RO) ===
The ontologies should use relations between items from the [[Relation Ontology|Relations Ontology (RO)]]. This ensures that different ontologies can integrated seamlessly, which is specially important for [[Semantic reasoner|logical inference]].<ref>{{Cite web|url=http://obofoundry.org/principles/fp-007-relations.html|title=Relations (principle 7)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should use relations between items from the [[Relation Ontology|Relations Ontology (RO)]]. This ensures that different ontologies can integrated seamlessly, which is specially important for [[Semantic reasoner|logical inference]].<ref>{{Cite web|url=http://obofoundry.org/principles/fp-007-relations.html|title=Relations (principle 7)|website=obofoundry.org|access-date=2020-02-06}}</ref>


The Relation Ontology (RO) is an [[Ontology (information science)|ontology]] designed to represent the [[Ontology components#Relationships|relationships]] between different biomedical concepts.<ref>{{Cite journal|last=Smith|first=Barry|last2=Ceusters|first2=Werner|last3=Klagges|first3=Bert|last4=Köhler|first4=Jacob|last5=Kumar|first5=Anand|last6=Lomax|first6=Jane|last7=Mungall|first7=Chris|last8=Neuhaus|first8=Fabian|last9=Rector|first9=Alan L|last10=Rosse|first10=Cornelius|date=2005|title=Relations in biomedical ontologies|url=http://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r46|journal=Genome Biology|volume=6|issue=5|pages=R46|doi=10.1186/gb-2005-6-5-r46|pmc=1175958|pmid=15892874}}</ref> It describes rigorously relations like "part_of", "located_in" and "preceded_by" that are reused by many OBO Foundry ontologies.
The Relation Ontology (RO) is an [[Ontology (information science)|ontology]] designed to represent the [[Ontology components#Relationships|relationships]] between different biomedical concepts.<ref>{{Cite journal|last1=Smith|first1=Barry|last2=Ceusters|first2=Werner|last3=Klagges|first3=Bert|last4=Köhler|first4=Jacob|last5=Kumar|first5=Anand|last6=Lomax|first6=Jane|last7=Mungall|first7=Chris|last8=Neuhaus|first8=Fabian|last9=Rector|first9=Alan L|last10=Rosse|first10=Cornelius|date=2005|title=Relations in biomedical ontologies|journal=Genome Biology|volume=6|issue=5|pages=R46|doi=10.1186/gb-2005-6-5-r46|pmc=1175958|pmid=15892874 |doi-access=free }}</ref> It describes rigorously relations like "part_of", "located_in" and "preceded_by" that are reused by many OBO Foundry ontologies.


==== Documentation ====
=== Documentation ===
OBO ontologies need to be thoroughly documented. Frequently this is done via [[GitHub]] repositories for each specific ontologies (see [[List of OBO Foundry ontologies]]).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-008-documented.html|title=Documentation (principle 8)|website=obofoundry.org|access-date=2020-02-06}}</ref>
OBO ontologies need to be thoroughly documented. Frequently this is done via [[GitHub]] repositories for each specific ontologies (see [[List of OBO Foundry ontologies]]).<ref>{{Cite web|url=http://obofoundry.org/principles/fp-008-documented.html|title=Documentation (principle 8)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Plurality of users ====
=== Plurality of users ===
The ontologies should be useful for multiple different people, and ontology developers should document the evidences of use. This criteria is important for the review process. Examples of use include linking to terms by other ontologies, use in [[Semantic Web|semantic web]] projects, use in [[annotation]]s or other research applications.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-009-users.html|title=Documented Plurality of Users (principle 9)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should be useful for multiple different people, and ontology developers should document the evidence of use. This criterion is important for the review process. Examples of use include linking to terms by other ontologies, use in [[Semantic Web|semantic web]] projects, use in [[annotation]]s or other research applications.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-009-users.html|title=Documented Plurality of Users (principle 9)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Openness to collaborations ====
=== Openness to collaborations ===
The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-010-collaboration.html|title=Commitment To Collaboration (principle 10)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-010-collaboration.html|title=Commitment To Collaboration (principle 10)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Locus of authority ====
=== Locus of authority ===
The ontologies should have one person responsible for the ontology who mediates interaction with the community.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-011-locus-of-authority.html|title=Locus of Authority (principle 11)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should have one person responsible for the ontology who mediates interaction with the community.<ref>{{Cite web|url=http://obofoundry.org/principles/fp-011-locus-of-authority.html|title=Locus of Authority (principle 11)|website=obofoundry.org|access-date=2020-02-06}}</ref>


==== Naming conventions ====
=== Naming conventions ===
Naming conventions for OBO ontologies aim at making primary labels unambiguous and unique inside the ontology (and preferably, inside OBO). Labels and synonyms should be written in English, avoiding the use of [[underscore]]s and [[camel case]].<ref>{{Cite web|url=http://obofoundry.org/principles/fp-012-naming-conventions.html|title=Naming Conventions (principle 12)|website=obofoundry.org|access-date=2020-02-06}}</ref> OBO lacks a mechanism for multilangual support, in contrats to [[Wikidata]], which allows labels in different systems. The naming system in OBO is based on a series of surveys at cataloguing naming conventions of current ontologies, as well as discover issues relating to these conventions.<ref>{{Cite journal|last=Schober|first=Daniel|last2=Smith|first2=Barry|last3=Lewis|first3=Suzanna E|last4=Kusnierczyk|first4=Waclaw|last5=Lomax|first5=Jane|last6=Mungall|first6=Chris|last7=Taylor|first7=Chris F|last8=Rocca-Serra|first8=Philippe|last9=Sansone|first9=Susanna-Assunta|date=2009|title=Survey-based naming conventions for use in OBO Foundry ontology development|url=http://dx.doi.org/10.1186/1471-2105-10-125|journal=BMC Bioinformatics|volume=10|issue=1|pages=125|doi=10.1186/1471-2105-10-125|issn=1471-2105|doi-access=free}}</ref>
Naming conventions for OBO ontologies aim at making primary labels unambiguous and unique inside the ontology (and preferably, inside OBO). Labels and synonyms should be written in English, avoiding the use of [[underscore]]s and [[camel case]].<ref>{{Cite web|url=http://obofoundry.org/principles/fp-012-naming-conventions.html|title=Naming Conventions (principle 12)|website=obofoundry.org|access-date=2020-02-06}}</ref> OBO lacks a mechanism for multilingual support, in contrast to [[Wikidata]], which allows labels in different systems. The naming system in OBO is based on a series of surveys at cataloguing naming conventions of current ontologies, as well as discover issues relating to these conventions.<ref>{{Cite journal|last1=Schober|first1=Daniel|last2=Smith|first2=Barry|last3=Lewis|first3=Suzanna E|last4=Kusnierczyk|first4=Waclaw|last5=Lomax|first5=Jane|last6=Mungall|first6=Chris|last7=Taylor|first7=Chris F|last8=Rocca-Serra|first8=Philippe|last9=Sansone|first9=Susanna-Assunta|date=2009|title=Survey-based naming conventions for use in OBO Foundry ontology development|journal=BMC Bioinformatics|volume=10|issue=1|pages=125|doi=10.1186/1471-2105-10-125|pmid=19397794|pmc=2684543|issn=1471-2105|doi-access=free}}</ref>


==== Maintenance ====
=== Maintenance ===
The ontologies should be updated with regards to changes in [[scientific consensus]]. The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame" <ref>{{Cite web|url=http://obofoundry.org/principles/fp-016-maintenance.html|title=Maintenance (principle 16)|website=obofoundry.org|access-date=2020-02-06}}</ref>
The ontologies should be updated with regards to changes in [[scientific consensus]]. The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame."<ref>{{Cite web|url=http://obofoundry.org/principles/fp-016-maintenance.html|title=Maintenance (principle 16)|website=obofoundry.org|access-date=2020-02-06}}</ref>


== See also ==
== See also ==
Line 130: Line 131:
*[https://metacpan.org/release/ONTO-PERL ONTO-PERL]
*[https://metacpan.org/release/ONTO-PERL ONTO-PERL]
*[https://web.archive.org/web/20120828100848/http://tagc.univ-mrs.fr/SimCT/ SimCT] Web-based tool to display relationships between biological objects annotated to an ontology in the form of a tree, based on their annotation similarity. On [[archive.org]]
*[https://web.archive.org/web/20120828100848/http://tagc.univ-mrs.fr/SimCT/ SimCT] Web-based tool to display relationships between biological objects annotated to an ontology in the form of a tree, based on their annotation similarity. On [[archive.org]]
*[https://web.archive.org/web/20080907194111/http://www.morphster.org/ Morphster Project] by University of Austin, Texax. On archive.org
*[https://web.archive.org/web/20080907194111/http://www.morphster.org/ Morphster Project] by University of Austin, Texas. On archive.org
* [http://www.obofoundry.org/ontology/ro.html Relation ontology on OBO Foundry].
* [http://www.obofoundry.org/ontology/ro.html Relation ontology on OBO Foundry].


Latest revision as of 17:40, 3 October 2023

OBO Foundry
FocusImprovent of biomedical ontologies
Members
27
Key people
Suzanna Lewis, Barry Smith, Michael Ashburner
Websiteobofoundry.org

The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences.[1] The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.

The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a phenotype in a mouse model and its related phenotype in zebrafish).[2]

Introduction[edit]

The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using controlled vocabularies. Ideally, such controlled vocabularies take the form of ontologies, which support logical reasoning over the data annotated using the terms in the vocabulary.

The formalization of concepts in the biomedical domain is especially known via the work of the Gene Ontology Consortium, a part of the OBO Foundry. This has led to the development of certain proposed principles of good practice in ontology development, which are now being put into practice within the framework of the Open Biomedical Ontologies consortium through its OBO Foundry initiative. OBO ontologies form part of the resources of the National Center for Biomedical Ontology, where they form a central component of the NCBO's BioPortal.

Open Biological and Biomedical Ontologies[edit]

The Open Biological and Biomedical Ontologies (OBO; formerly Open Biomedical Ontologies) is an effort to create ontologies (controlled vocabularies) for use across biological and medical domains. A subset of the original OBO ontologies has started the OBO Foundry, which leads the OBO efforts since 2007.[1]

The creation of OBO in 2001 was largely inspired by the efforts of the Gene Ontology project.[3] OBO forms part of the resources of the U.S. National Center for Biomedical Ontology (NCBIO) and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.

Rules for participation[edit]

The OBO Foundry is open to participations of any interested individuals. Ontologies that intend to be officially part of the OBO Foundry have to adhere to the OBO principles and pass a series of reviews done by the members, when "the Foundry coordinators serve as analogs of journal editors".[1] There are ontologies that follow OBO principles but are not officially part of OBO, such as eagle-i's Reagent Application Ontology.[4] and the Animals in Context Ontology.[5]

An integration into OBO of the OntoClean's theory of rigidity has been proposed as a step to standardize candidate ontologies. This integration would make it easier to develop software to automatically check candidates.[6]

Tools[edit]

The OBO Foundry community is also dedicated to developing tools to facilitate creating and maintaining ontologies. Most ontology developers in OBO use the Protégé ontology editor and the Web Ontology Language (OWL) for building ontologies. To facilitate command line management of ontologies in a Protégé- and OWL-compatible format, the OBO Foundry has developed the tool ROBOT (ROBOT is an OBO Tool). ROBOT aggregates functions for routine tasks in ontology development, is open source, and can be used either via the command line or as a library for any language on the Java Virtual Machine.[7]

Other tool related to the OBO effort is OBO-Edit,[8] an ontology editor and reasoner funded by the Gene Ontology Consortium. There are also plugins for OBO-Edit which facilitate the development of ontologies, such as the semi-automatic ontology generator DOG4DAG.[9]

The OBO file format[edit]

The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of Web Ontology Language (OWL).

As a community effort, standard common mappings have been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL.[10][11] The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.[12]

OBO Foundry Ontologies[edit]

The initial set of OBO Foundry ontologies was composed by mature ontologies (such as the Gene Ontology, GO, and the Foundational Model of Anatomy, FMAO), by mergers of previously existing ontologies (ex: the Cell Ontology,[13] CL, formed from different dedicated ontologies,[14][15] and related parts on GO and FMAO) and by development of new ontologies based on its principles.[16]

The original set of ontologies also included the Zebrafish Anatomical Ontology[17] (a part of the Zebrafish Information Network), the CheBI ontology, the Disease Ontology, the Plant Ontology, the Sequence Ontology, the Ontology for Biomedical Investigations and the Protein Ontology.[16]

The number of ontologies in OBO has grown to the order of hundreds, and they are gathered in the list of OBO Foundry ontologies.

OBO Foundry and Wikidata[edit]

A number of different OBO Foundry ontologies have also been integrated to the Wikidata knowledge graph.[18][19] This has led to the integration of OBO structured ontologies to data from other, non-OBO databases . For example, the integration of the Human Disease Ontology[20] to Wikidata has enabled its link to the description of cell-lines from the resource Cellosaurus.[21] One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies. Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise).[22]

Principles[edit]

Summary of OBO Foundry Principles[23] for development of an OBO-compatible life sciences ontology:

Openness[edit]

The ontologies are openly available and have to be released under either the license CC-BY 3.0 or under the public domain (CC0).[24] The openness of the ontologies has enabled, for example, the import of terms from the Gene Ontology (one of the ontologies that follow OBO Principles) to the Wikidata project.[25]

Common format[edit]

The ontologies have to be available in a common formal language. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/OWL2 or OBO using a RDF/XML syntax to maximize interoperability.[26]

Orthogonality[edit]

Mapping from OBO IDs to OBO Unified Resource Identifiers (URIs), unique for each item.[10]

Terms should be unique in the OBO space, meaning that each item has a unique ontology prefix (such as CHEBI, GO, PRO) and a local numeric identifier within the ontology.[27] The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.[28] In order to participate in OBO Foundry, ontologies have to be orthogonal and the concepts it models must be unique within OBO, so each concept has a single Uniform Resource Identifier (URI). New ontologies have, then, to reuse work done in other efforts.[28]

Despite the ideal of uniqueness of terms and interoperability, in practice, this is difficult to enforce, leading to the occurrence of term duplication. Furthermore, some ontologies do not reuse terms or even reuse terms inappropriately.[29]

Versioning[edit]

Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains.[30] In order to ensure that new versions are updated, but tools that use older version of the ontologies are still function, OBO enforces a system of versioning systems, with each ontology version receiving a unique identifier, either in the format of a date or a numbering system, and metadata dags.[31]

Scope[edit]

The ontologies should have a clearly specified scope (the domain it intends to cover).[32]

Have textual definitions[edit]

The ontologies should have textual definitions for each item, in a human-readable way. That means that beside the alphanumeric identification for each item, they should be described in natural language by logical affirmations following the Aristotelian logic in a way that is unique within the ontology.[33]

Standardized relations and the Relation Ontology (RO)[edit]

The ontologies should use relations between items from the Relations Ontology (RO). This ensures that different ontologies can integrated seamlessly, which is specially important for logical inference.[34]

The Relation Ontology (RO) is an ontology designed to represent the relationships between different biomedical concepts.[35] It describes rigorously relations like "part_of", "located_in" and "preceded_by" that are reused by many OBO Foundry ontologies.

Documentation[edit]

OBO ontologies need to be thoroughly documented. Frequently this is done via GitHub repositories for each specific ontologies (see List of OBO Foundry ontologies).[36]

Plurality of users[edit]

The ontologies should be useful for multiple different people, and ontology developers should document the evidence of use. This criterion is important for the review process. Examples of use include linking to terms by other ontologies, use in semantic web projects, use in annotations or other research applications.[37]

Openness to collaborations[edit]

The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.[38]

Locus of authority[edit]

The ontologies should have one person responsible for the ontology who mediates interaction with the community.[39]

Naming conventions[edit]

Naming conventions for OBO ontologies aim at making primary labels unambiguous and unique inside the ontology (and preferably, inside OBO). Labels and synonyms should be written in English, avoiding the use of underscores and camel case.[40] OBO lacks a mechanism for multilingual support, in contrast to Wikidata, which allows labels in different systems. The naming system in OBO is based on a series of surveys at cataloguing naming conventions of current ontologies, as well as discover issues relating to these conventions.[41]

Maintenance[edit]

The ontologies should be updated with regards to changes in scientific consensus. The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame."[42]

See also[edit]

References[edit]

  1. ^ a b c Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–5. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687.
  2. ^ Mungall, Christopher J; Gkoutos, Georgios V; Smith, Cynthia L; Haendel, Melissa A; Lewis, Suzanna E; Ashburner, Michael (2010). "Integrating phenotype ontologies across multiple species". Genome Biology. 11 (1): R2. doi:10.1186/gb-2010-11-1-r2. ISSN 1465-6906. PMC 2847714. PMID 20064205.
  3. ^ Shimoyama, Mary; Dwinell, Melinda; Jacob, Howard (2009-08-05). "Multiple Ontologies for Integrating Complex Phenotype Datasets". Nature Precedings. doi:10.1038/npre.2009.3554. ISSN 1756-0357.
  4. ^ Brush MH, Vasilevsky N, Torniai C, Johnson T, Shaffer C, Haendel M (2011). "Developing a reagent application ontology within the OBO foundry framework". CEUR Workshop Proceedings. 833: 234–236.
  5. ^ Santamaria SL (2012). Development the Animals in Context ontology (PDF). Proceedings of the International Conference on Biomedical Ontology. Graz.
  6. ^ Seyed, Patrice, and Stuart C. Shapiro. (2011). Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies (PDF). Proceedings of the International Conference on Biomedical Ontology (CEUR 993).{{cite conference}}: CS1 maint: multiple names: authors list (link)
  7. ^ Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA (July 2019). "ROBOT: A Tool for Automating Ontology Workflows". BMC Bioinformatics. 20 (1): 407. doi:10.1186/s12859-019-3002-3. PMC 6664714. PMID 31357927.
  8. ^ Day-Richter J, Harris MA, Haendel M, Lewis S (August 2007). "OBO-Edit--an ontology editor for biologists". Bioinformatics. 23 (16): 2198–200. doi:10.1093/bioinformatics/btm112. PMID 17545183.
  9. ^ Wächter T, Schroeder M (June 2010). "Semi-automated ontology generation within OBO-Edit". Bioinformatics. 26 (12): i88-96. doi:10.1093/bioinformatics/btq188. PMC 2881373. PMID 20529942.
  10. ^ a b Tirmizi, Syed; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P (2011). "Mapping between the OBO and OWL ontology languages". Journal of Biomedical Semantics. 2 (Suppl 1): S3. doi:10.1186/2041-1480-2-s1-s3. ISSN 2041-1480. PMC 3105495. PMID 21388572.
  11. ^ Golbreich, Christine; Horridge, Matthew; Horrocks, Ian; Motik, Boris; Shearer, Rob (2007), "OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences", The Semantic Web, Lecture Notes in Computer Science, vol. 4825, Springer Berlin Heidelberg, pp. 169–182, Bibcode:2007LNCS.4825..169G, doi:10.1007/978-3-540-76298-0_13, ISBN 978-3-540-76297-3
  12. ^ Antezana, E.; Egana, M.; De Baets, B.; Kuiper, M.; Mironov, V. (2008). "ONTO-PERL: An API for supporting the development and analysis of bio-ontologies". Bioinformatics. 24 (6): 885–887. doi:10.1093/bioinformatics/btn042. PMID 18245124.
  13. ^ Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M.; Brush, Matthew H.; Dahdul, Wasila M.; Dougall, David S.; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E. (2016-07-04). "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability". Journal of Biomedical Semantics. 7 (1): 44. doi:10.1186/s13326-016-0088-7. ISSN 2041-1480. PMC 4932724. PMID 27377652.
  14. ^ Bard, Jonathan; Rhee, Seung Y.; Ashburner, Michael (2005-01-14). "An ontology for cell types". Genome Biology. 6 (2): R21. doi:10.1186/gb-2005-6-2-r21. ISSN 1474-760X. PMC 551541. PMID 15693950.
  15. ^ Kelso, J. (2003-05-12). "eVOC: A Controlled Vocabulary for Unifying Gene Expression Data". Genome Research. 13 (6): 1222–1230. doi:10.1101/gr.985203. ISSN 1088-9051. PMC 403650. PMID 12799354.
  16. ^ a b Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J; Leontis, Neocles (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–1255. doi:10.1038/nbt1346. ISSN 1087-0156. PMC 2814061. PMID 17989687.
  17. ^ Van Slyke, Ceri E.; Bradford, Yvonne M.; Westerfield, Monte; Haendel, Melissa A. (2014-02-25). "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio". Journal of Biomedical Semantics. 5 (1): 12. doi:10.1186/2041-1480-5-12. ISSN 2041-1480. PMC 3944782. PMID 24568621.
  18. ^ Waagmeester, Andra; Stupp, Gregory; Burgstaller-Muehlbacher, Sebastian; Good, Benjamin M; Griffith, Malachi; Griffith, Obi L; Hanspers, Kristina; Hermjakob, Henning; Hudson, Toby S; Hybiske, Kevin; Keating, Sarah M (2020-03-17). Rodgers, Peter; Mungall, Chris (eds.). "Wikidata as a knowledge graph for the life sciences". eLife. 9: e52614. doi:10.7554/eLife.52614. ISSN 2050-084X. PMC 7077981. PMID 32180547.
  19. ^ Turki, Houcemeddine; Shafee, Thomas; Hadj Taieb, Mohamed Ali; Ben Aouicha, Mohamed; Vrandečić, Denny; Das, Diptanshu; Hamdi, Helmi (2019-11-01). "Wikidata: A large-scale collaborative ontological medical database". Journal of Biomedical Informatics. 99: 103292. doi:10.1016/j.jbi.2019.103292. ISSN 1532-0464. PMID 31557529.
  20. ^ Schriml, Lynn M.; Mitraka, Elvira; Munro, James; Tauber, Becky; Schor, Mike; Nickle, Lance; Felix, Victor; Jeng, Linda; Bearer, Cynthia; Lichenstein, Richard; Bisordi, Katharine (2019-01-08). "Human Disease Ontology 2018 update: classification, content and workflow expansion". Nucleic Acids Research. 47 (D1): D955–D962. doi:10.1093/nar/gky1032. ISSN 0305-1048. PMC 6323977. PMID 30407550.
  21. ^ "HeLa". www.wikidata.org. Retrieved 2020-05-04.
  22. ^ Jacobsen, Annika; Waagmeester, Andra; Kaliyaperumal, Rajaram; Stupp, Gregory S.; M. Schriml, Lynn; Thompson, Mark; I. Su, Andrew; Roos, Marco (2018-12-04). "Wikidata as an intuitive resource towards semantic data modeling in data FAIRification". Figshare. doi:10.6084/m9.figshare.7415282.v2.
  23. ^ "Overview". obofoundry.org. Retrieved 2020-02-06.
  24. ^ "Open (principle 1)". obofoundry.org. Retrieved 2020-02-06.
  25. ^ Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, et al. (2016-01-01). "Wikidata as a semantic framework for the Gene Wiki initiative". Database. 2016: baw015. doi:10.1093/database/baw015. PMC 4795929. PMID 26989148.
  26. ^ "Common Format (principle 2)". obofoundry.org. Retrieved 2020-02-06.
  27. ^ "URI/Identifier Space (principle 3)". obofoundry.org. Retrieved 2020-02-06.
  28. ^ a b Courtot M, Mungall C, Brinkman RR, Ruttenberg A (2010). Building the OBO Foundry-One Policy at a Time. CEURS Proceedings: International Conference on Biomedical Ontologies.
  29. ^ Ghazvinian A, Noy NF, Musen MA (May 2011). "How orthogonal are the OBO Foundry ontologies?". Journal of Biomedical Semantics. 2 (Suppl 2): S2. doi:10.1186/2041-1480-2-s2-s2. PMC 3102891. PMID 21624157.
  30. ^ Groß, Anika; Pruski, Cédric; Rahm, Erhard (2016). "Evolution of biomedical ontologies and mappings: Overview of recent approaches". Computational and Structural Biotechnology Journal. 14: 333–340. doi:10.1016/j.csbj.2016.08.002. ISSN 2001-0370. PMC 5018063. PMID 27642503.
  31. ^ "Versioning (principle 4)". obofoundry.org. Retrieved 2020-02-06.
  32. ^ "Scope (principle 5)". obofoundry.org. Retrieved 2020-02-06.
  33. ^ "Textual Definitions (principle 6)". obofoundry.org. Retrieved 2020-02-06.
  34. ^ "Relations (principle 7)". obofoundry.org. Retrieved 2020-02-06.
  35. ^ Smith, Barry; Ceusters, Werner; Klagges, Bert; Köhler, Jacob; Kumar, Anand; Lomax, Jane; Mungall, Chris; Neuhaus, Fabian; Rector, Alan L; Rosse, Cornelius (2005). "Relations in biomedical ontologies". Genome Biology. 6 (5): R46. doi:10.1186/gb-2005-6-5-r46. PMC 1175958. PMID 15892874.
  36. ^ "Documentation (principle 8)". obofoundry.org. Retrieved 2020-02-06.
  37. ^ "Documented Plurality of Users (principle 9)". obofoundry.org. Retrieved 2020-02-06.
  38. ^ "Commitment To Collaboration (principle 10)". obofoundry.org. Retrieved 2020-02-06.
  39. ^ "Locus of Authority (principle 11)". obofoundry.org. Retrieved 2020-02-06.
  40. ^ "Naming Conventions (principle 12)". obofoundry.org. Retrieved 2020-02-06.
  41. ^ Schober, Daniel; Smith, Barry; Lewis, Suzanna E; Kusnierczyk, Waclaw; Lomax, Jane; Mungall, Chris; Taylor, Chris F; Rocca-Serra, Philippe; Sansone, Susanna-Assunta (2009). "Survey-based naming conventions for use in OBO Foundry ontology development". BMC Bioinformatics. 10 (1): 125. doi:10.1186/1471-2105-10-125. ISSN 1471-2105. PMC 2684543. PMID 19397794.
  42. ^ "Maintenance (principle 16)". obofoundry.org. Retrieved 2020-02-06.

External links[edit]

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