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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 }}</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 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 }}</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}}</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|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}}</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>


==== Scope ====
;Scope: The ontologies should have a clearly especified 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 especified 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 unique textual definitions for each item, in a [[Human-readable medium|human-readable]] way.<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 unique textual definitions for each item, in a [[Human-readable medium|human-readable]] way.<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 ====
;Standardized relations: The ontologies should use relations between items from the [[Relation Ontology|Relations Ontology (RO)]].<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)]].<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>


==== 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.<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 evidences of use.<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: <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>


;Maintenance: The ontologies should be updated with regards to changes in scientific consensus.<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>
:<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>

==== Maintenance ====
⚫
The ontologies should be updated with regards to changes in scientific consensus.<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>

⚫
Tools


⚫
== Tools ==
The OBO Foundry community is also dedicated to develop tools to faciliate 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 develop tools to faciliate 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>


Revision as of 13:54, 1 April 2020

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] and it is behind the 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 ontologies that follow the OBO Foundry principles.

Introduction

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. Thehas 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.

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". [1] There are ontologies that follow OBO principles but are not officially part of OBO, such as eagle-i's Reagent Application Ontology.[2]

Principles

Summary of OBO Foundry Principles[3] for development of an OBO-compatible life sciences ontology:

Openess

The ontologies are openly available and have to be released under either the license CC-BY 3.0 or under the public domain (CC0).[4] 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.[5]

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/OWL2 or OBO using a RDF/XML syntax to maximize interoperability.[6]

Orthogonality

Terms should be unique in the OBO space, meaning that each item has an unique ontology prefix (such as CHEBI, GO, PRO) and a local numeric identifier within the ontology.[7] The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.[8] 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.[8]

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. [9]

Versioning

Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains[10]. 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.[11]

Scope

The ontologies should have a clearly especified scope (the domain it intends to cover).[12]

Have textual definitions

The ontologies should have unique textual definitions for each item, in a human-readable way.[13]

Standardized relations

The ontologies should use relations between items from the Relations Ontology (RO).[14]

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).[15]

Plurality of users

The ontologies should be useful for multiple different people, and ontology developers should document the evidences of use.[16]

Openness to collaborations

The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.[17]

Locus of authority

The ontologies should have one person responsible for the ontology who mediates interaction with the community.[18]

Naming conventions

[19]

Maintenance

The ontologies should be updated with regards to changes in scientific consensus.[20]

Tools

The OBO Foundry community is also dedicated to develop tools to faciliate 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 and 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.[21]

Other tool related to the OBO effort is OBO-Edit[22], 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.[23]

See also

References

  1. ^ a b 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. ^ Brush, Matthew H.; Vasilevsky, Nicole; Torniai, Carlo; Johnson, Tenille; Shaffer, Christopher; Haendel, Melissa (2011). "Developing a reagent application ontology within the OBO foundry framework". CEUR Workshop Proceedings: 234–236. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  3. ^ "Overview". obofoundry.org. Retrieved 2020-02-06.
  4. ^ "Open (principle 1)". obofoundry.org. Retrieved 2020-02-06.
  5. ^ 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. doi:10.1093/database/baw015. PMC 4795929. PMID 26989148.
  6. ^ "Common Format (principle 2)". obofoundry.org. Retrieved 2020-02-06.
  7. ^ "URI/Identifier Space (principle 3)". obofoundry.org. Retrieved 2020-02-06.
  8. ^ a b Courtot, Mélanie; Mungall, Christopher; Brinkman RR; Ruttenberg, Alan (2010). Building the OBO Foundry-One Policy at a Time. CEURS Proceedings: International Conference on Biomedical Ontologies. {{cite conference}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  9. ^ Ghazvinian A, Noy NF, Musen MA (May 2011). "How orthogonal are the OBO Foundry ontologies?". Journal of Biomedical Semantics. 2 Suppl 2 (Suppl 2): S2. doi:10.1186/2041-1480-2-s2-s2. PMID 21624157.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  10. ^ 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.
  11. ^ "Versioning (principle 4)". obofoundry.org. Retrieved 2020-02-06.
  12. ^ "Scope (principle 5)". obofoundry.org. Retrieved 2020-02-06.
  13. ^ "Textual Definitions (principle 6)". obofoundry.org. Retrieved 2020-02-06.
  14. ^ "Relations (principle 7)". obofoundry.org. Retrieved 2020-02-06.
  15. ^ "Documentation (principle 8)". obofoundry.org. Retrieved 2020-02-06.
  16. ^ "Documented Plurality of Users (principle 9)". obofoundry.org. Retrieved 2020-02-06.
  17. ^ "Commitment To Collaboration (principle 10)". obofoundry.org. Retrieved 2020-02-06.
  18. ^ "Locus of Authority (principle 11)". obofoundry.org. Retrieved 2020-02-06.
  19. ^ "Naming Conventions (principle 12)". obofoundry.org. Retrieved 2020-02-06.
  20. ^ "Maintenance (principle 16)". obofoundry.org. Retrieved 2020-02-06.
  21. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  22. ^ 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.
  23. ^ Wächter T, Schroeder M (June 2010). "Semi-automated ontology generation within OBO-Edit". Bioinformatics. 26 (12): i88-96. doi:10.1093/bioinformatics/btq188. PMID 20529942.

Further reading

External links

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