To support practical application and mapping
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Many ontologies in the Disease, Phenotype and Experimental Investigation domains have textual definitions (vocabulary) for class terms which makes them more likely to bring unique value for application. A high proportion of quality textual definitions will facilitate interoperability through mapping the meaning (semantics) of equivalence in different ontologies.
3.13. Naming conventions
Naming conventions used by ontology providers tend to be a heterogeneous and inconsistent. This is because names emerge often in an ad hoc manner rather than through an agreed nomenclature. Of course there are exceptions which are much more mature and consistent, such as the HUGO Gene Nomenclature Committee which provides the authoritative source of human gene names (http://www.genenames.org). Another excellent example is Chemical Entities of Biological Entities (ChEBI) which started as a curated nomenclature for small molecules and has developed into a mature ontology in the OBO Foundry. The OBO principle wiki page, FP_012_naming_conventions (http://wiki.obofoundry.org/wiki/index.php/FP_012_naming_conventions) is under development and mostly mentions the publication entitled "Survey-based naming conventions for use in OBO Foundry ontology development” by Schober et al 2009 (http://www.biomedcentral.com/1471-2105/10/125). This guideline aligns with Malone et al 2016 Rule 5: Textual Definitions Should Be Written for Domain Experts.
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| Guideline | OBO Principle | 10 Rules of Malone et al 2016 |
|---|---|---|
1.Format | http://www.obofoundry.org/principles/fp-002-format.html | |
| 2.URIs | http://wikiwww.obofoundry.org/wiki/index.php/FP_003_URIsprinciples/fp-003-uris.html | Rule 3: The Ontology Classes and Relationships Should Persist. |
| 3.Versioning | http://wikiwww.obofoundry.org/wiki/index.php/FP_004_versioningprinciples/fp-004-versioning.html | Rule 8: Previous Versions Should Be Available |
| 4.Documentation | http://wikiwww.obofoundry.org/wiki/index.php/FP_008_documentedprinciples/fp-008-documented.html | |
| 5.Users | http://wikiwww.obofoundry.org/wiki/index.php/FP_009_usersprinciples/fp-009-users.html | Rule 6: The Ontology Should Be Developed by the Community but Not Incapacitated by It |
| 6.Authority | http://wikiwww.obofoundry.org/wiki/index.php/FP_011_locus_of_authorityprinciples/fp-011-locus-of-authority.html | Rule 6: The Ontology Should Be Developed by the Community but Not Incapacitated by It |
| 7.Maintenance | http://wikiwww.obofoundry.org/wiki/index.php/FP_016_maintenanceprinciples/fp-016-maintenance.html | Rule 7: The Ontology Should Be under Active Development |
| 8.License | http://wikiwww.obofoundry.org/wiki/index.php/FP_001_openprinciples/fp-001-open.html | Rule 9: Open Data Requires Open Ontologies |
| 9.Content delineation | http://wikiwww.obofoundry.org/wiki/index.php/FP_005_delineated_contentprinciples/fp-005-delineated-content.html | Rule 1: The Ontology Should Be about a Specific Domain of Knowledge |
| 10.Content coverage | http://www.obofoundry.org/principles/fp-005-delineated-content.html | Rule 2: The Ontology Should Reflect Current Understanding of Biological Systems |
| 11.Content quality | Rule 2: The Ontology Should Reflect Current Understanding of Biological Systems | |
| 12.Textual definitions | http://wikiwww.obofoundry.org/wiki/index.php/FP_006_textual_definitionsprinciples/fp-006-textual-definitions.html | Rule 4: Classes Should Contain Textual Definitions |
| 13.Naming conventions | http://wikiwww.obofoundry.org/wiki/index.php/FP_012_naming_conventionsprinciples/fp-012-naming-conventions.html | Rule 5: Textual Definitions Should Be Written for Domain Experts |
| 14.Relations | http://wikiwww.obofoundry.org/wiki/index.php/FP_007_relationsprinciples/fp-007-relations.html | |
| 15.Conserved URIs | http://www.obofoundry.org/principles/fp-010-collaboration.html |
6. References
- The Open Biological and Biomedical Ontologies (OBO) Foundry (http://www.obofoundry.org)
- NCBO BioPortal (http://bioportal.bioontology.org)
- "Survey-based naming conventions for use in OBO Foundry ontology development” by Schooner et al 2009 (http://www.biomedcentral.com/1471-2105/10/125)
- Arp, Smith and Spear: Building Ontologies with Basic Formal Ontology published by MIT Press, August 17, 2015
- Malone et al "Ten Simple Rules for Selecting a Bio-ontology" PLOS: Computational Biology 2016 DOI:10.1371/journal.pcbi 1004743.