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== 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|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>
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|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>


<br />
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">{{Cite journal|last=Courtot|first=Mélanie|last2=Mungall|first2=Christopher|last3=Brinkman RR|last4=Ruttenberg|first4=Alan|date=|year=2010|title=Building the OBO Foundry-One Policy at a Time|url=|journal=CEURS Proceedings: International Conference on Biomedical Ontologies|volume=|pages=|via=}}</ref><br />


== Principles ==
== Principles ==
Line 46: Line 47:
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 =====
⚫
#'''[[Open-source software|Be open]]:''' 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>
#'''Use a common format:''' the ontologies have to be available at least in the formats OWL, [[Web Ontology Language|OWL2]] or [[Open Biomedical Ontologies#The OBO file format|OBO]] 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 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>

⚫
#'''Respect the URI/Identifier Space:''' terms are 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" />
===== Common format =====
⚫
#'''Have its [[Software versioning|versioning]] documented:''' ontologies evolve in time, and consequently OBO ontologies to have proper guidelines for updates.<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>
#'''Have a 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 have to be available at least in the formats OWL, [[Web Ontology Language|OWL2]] or [[Open Biomedical Ontologies#The OBO file format|OBO]] 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>

⚫
#'''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>
===== Orthogonality =====
⚫
#'''Use 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>
⚫
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 journal|last=Courtot|first=Mélanie|last2=Mungall|first2=Christopher|last3=Brinkman RR|last4=Ruttenberg|first4=Alan|date=|year=2010|title=Building the OBO Foundry-One Policy at a Time|url=|journal=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" />
⚫
#'''Be thoroughly documented.''' <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>

⚫
#'''Be used by multiple 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>
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|last=Ghazvinian|first=Amir|last2=Noy|first2=Natalya F|last3=Musen|first3=Mark A|date=2011|title=How orthogonal are the OBO Foundry ontologies?|url=http://dx.doi.org/10.1186/2041-1480-2-s2-s2|journal=Journal of Biomedical Semantics|volume=2|issue=Suppl 2|pages=S2|doi=10.1186/2041-1480-2-s2-s2|issn=2041-1480}}</ref>
⚫
#'''Be open 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>

⚫
#'''Have someone responsible for it:''' 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>
'''[[Software versioning|Versioning]]'''
⚫
#'''Follow 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>

⚫
#'''Be mantained over time:''' 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>
⚫
Ontologies evolve in time, and consequently OBO ontologies to have proper guidelines for updates .<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'''

⚫
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'''

⚫
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:'''

⚫
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''' <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]]).

'''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>

'''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>

'''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>

⚫
'''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>


== Tools ==
== Tools ==

Revision as of 21:55, 28 March 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]

Common format

The ontologies have to be available at least in the formats OWL, OWL2 or OBO to maximize interoperability.[5]

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.[6] The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.[7] 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.[7]

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. [8]

Versioning

Ontologies evolve in time, and consequently OBO ontologies to have proper guidelines for updates .[9]

Scope

The ontologies should have a clearly especified scope (the domain it intends to cover).[10]

Have textual definitions

The ontologies should have unique textual definitions for each item, in a human-readable way.[11]

Standardized relations:

The ontologies should use relations between items from the Relations Ontology (RO).[12]

Documentation [13]

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

Plurality of users

The ontologies should be useful for multiple different people, and ontology developers should document the evidences of use.[14]

Openness to collaborations

The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.[15]

Locus of authority

The ontologies should have one person responsible for the ontology who mediates interaction with the community.[16]

Naming conventions [17]

Maintenance

The ontologies should be updated with regards to changes in scientific consensus.[18]

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.[19]

Other tool related to the OBO effort is OBO-Edit[20], 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.[21]

See also

References

  1. ^ a b The OBI Consortium; Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J (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.
  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.
  3. ^ "Overview". obofoundry.org. Retrieved 2020-02-06.
  4. ^ "Open (principle 1)". obofoundry.org. Retrieved 2020-02-06.
  5. ^ "Common Format (principle 2)". obofoundry.org. Retrieved 2020-02-06.
  6. ^ "URI/Identifier Space (principle 3)". obofoundry.org. Retrieved 2020-02-06.
  7. ^ 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.
  8. ^ Ghazvinian, Amir; Noy, Natalya F; Musen, Mark A (2011). "How orthogonal are the OBO Foundry ontologies?". Journal of Biomedical Semantics. 2 (Suppl 2): S2. doi:10.1186/2041-1480-2-s2-s2. ISSN 2041-1480.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  9. ^ "Versioning (principle 4)". obofoundry.org. Retrieved 2020-02-06.
  10. ^ "Scope (principle 5)". obofoundry.org. Retrieved 2020-02-06.
  11. ^ "Textual Definitions (principle 6)". obofoundry.org. Retrieved 2020-02-06.
  12. ^ "Relations (principle 7)". obofoundry.org. Retrieved 2020-02-06.
  13. ^ "Documentation (principle 8)". obofoundry.org. Retrieved 2020-02-06.
  14. ^ "Documented Plurality of Users (principle 9)". obofoundry.org. Retrieved 2020-02-06.
  15. ^ "Commitment To Collaboration (principle 10)". obofoundry.org. Retrieved 2020-02-06.
  16. ^ "Locus of Authority (principle 11)". obofoundry.org. Retrieved 2020-02-06.
  17. ^ "Naming Conventions (principle 12)". obofoundry.org. Retrieved 2020-02-06.
  18. ^ "Maintenance (principle 16)". obofoundry.org. Retrieved 2020-02-06.
  19. ^ Jackson, Rebecca C.; Balhoff, James P.; Douglass, Eric; Harris, Nomi L.; Mungall, Christopher J.; Overton, James A. (2019-07-29). "ROBOT: A Tool for Automating Ontology Workflows". BMC Bioinformatics. 20 (1): 407. doi:10.1186/s12859-019-3002-3. ISSN 1471-2105. PMC 6664714. PMID 31357927.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  20. ^ Day-Richter, J.; Harris, M. A.; Haendel, M.; Lewis, S. (2007-06-01). "OBO-Edit an ontology editor for biologists". Bioinformatics. 23 (16): 2198–2200. doi:10.1093/bioinformatics/btm112. ISSN 1367-4803. PMID 17545183.
  21. ^ Wächter, Thomas; Schroeder, Michael (2010-06-01). "Semi-automated ontology generation within OBO-Edit". Bioinformatics. 26 (12): i88–i96. doi:10.1093/bioinformatics/btq188. ISSN 1460-2059. PMID 20529942.

Further reading

  • M Courtot, C Mungall, RR Brinkman, A Ruttenberg, '[ceur-ws.org/Vol-833/paper72.pdf Building the OBO Foundry-One Policy at a Time]", Proceedings of the International Conference on Biomedical Ontology, (CEUR 993), 2011.
  • Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008;36:D344–D350.
  • A Ghazvinian, NF Noy, MA Musen","How orthogonal are the OBO Foundry ontologies", J Biomed Semantics 2011; 2(Suppl 2): S2. doi:10.1186/2041-1480-2-S2-S22011
  • CJ Mungall, GV Gkoutos, CL Smith, et al., "Integrating phenotype ontologies across multiple species", Genome Biology 2010, 11:R2 doi:10.1186/gb-2010-11-1-r2
  • SL Santamaria, "Development the Animals in Context ontology", Proceedings of the International Conference on Biomedical Ontology, Graz, 2012.
  • D Schober, B Smith, SE Lewis, W Kusnierczyk et al. "Survey-based naming conventions for use in OBO Foundry ontology development", BMC Bioinformatics 2009, 10:125 doi:10.1186/1471-2105-10-125
  • P Seyed, SC Shapiro, "[ceur-ws.org/Vol-833/paper23.pdf Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies]", Proceedings of the International Conference on Biomedical Ontology (CEUR 993), 2011.
  • CF Taylor, D Field, S-A Sansone, R Apweiler, M Ashburner, et al. “Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project”, Nature Biotechnology, 26 (2008), 889-896. PMC 2771753

External links

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