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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5. Appendices

5.1 Application of the guidelines Guidelines to a checklist

Pistoia Alliance Guidelines checklist for disease phenotype experimental investigation ontologies.xlsx

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