OBO Foundry

Technical Considerations

Ensure the ontology is logically consistent (tracker item)
- The ontology MUST be logically consistent; that is:
  - (a) there MUST NOT be contradictory statements revealed by reasoning;
  - (b) there MUST NOT be any unsatisfiable classes; and
  - (c) there MUST NOT be any circular definitions.
- This includes when the ontology is classified together with RO, BFO, and COB
- This also includes when the ontology is classified together with its base dependencies; that is, as part of a ‘full’ release (see Release Considerations section below)
Indicate the root terms of the ontology (tracker item)
- Some ontology browsers make use of an ontology-wide annotation property, ‘has ontology root term’ (IAO:0000700), that governs how the hierarchy is displayed. This helps shield users from having to navigate through not-specific-enough parent terms (such as BFO:0000040 “material entity”). To enable this feature, an ontology SHOULD specify one or more appropriate root terms like so:
```
  OWL format:
     <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/*root term ID*"/>
  OBO format:
     property_value: IAO:0000700 *root term ID*
```
Use standard synonym types
- Ontologies often include alternatives to term labels (aka synonyms). These can include abbreviations, acronyms, spelling variants, and other types of synonyms. A list of standard synonym types is provided by OMO under the parent Annotation Propery ‘SynonymTypeProperty’. Ontology developers that wish to indicate a specific type of synonym SHOULD first consult this list before minting their own. If it is necessary to create a new type, developers SHOULD consider submitting to the OMO controlled vocabulary list indicated above.

Content Considerations

Use the preferred source for imported terms
- Imported terms SHOULD be drawn from the ontology that is the preferred source for the term. The preferred source is usually the ontology with the same ID space as the term, but it can instead be the ontology that currently maintains the term. Importing a term from a secondary source is not recommended because there is no guarantee that the secondary source has the most up-to-date term information, and thus drawing from the original would avoid possible conflicts due to term divergence.
Import entire ontologies only when necessary (tracker item)
- Unless necessary, an entire ontology SHOULD NOT be imported if only a subset of terms is needed. To import terms on an individual basis, ROBOT ‘extract’ and OntoFox are useful tools. Notable exceptions are imports of small ontologies that provide upper level structure or useful sets of properties:
  - BFO (Basic Formal Ontology) or COB (Core Ontology for Biology and Biomedicine) are upper level ontologies used to harmonize multiple OBO Foundry ontologies under the same hierarchy.
  - OMO contains commonly used annotation properties.
  - RO Core contains the most commonly used relations.
Use of NCIt terms - If an ontology developer wishes to create a term with a label that already exists in NCIt, the following apply:
- If the NCIt term definition and hierarchical position are reasonable, that term SHOULD be used instead;
- If either the NCIt term definition or the hierarchical position are sub-optimal, the developer MAY create a term in the ontology with an identical label but with a revised definition and subclassing; alternatively such a term MAY be requested of another ontology, if appropriate;
- For case (b), if the definition is based on the NCIt definition, the new term MUST be linked to the original NCIt term to conform to the NCIt license requirements. Note: this does not apply to reuse of term labels.

Release Considerations

Provide recommended release types (tracker item)
- In addition to a set of standards pertaining to release format (see Principle 2), the following are the standards pertaining to release types, each of which differ with respect to imports, axiomization, and reasoning (see Release Artefacts for more detailed information):
- base (RECOMMENDED; denoted by PURL ending with ONT.owl): Content includes only terms that are owned by the ontology, which include (a) terms using that ontology’s prefix; and (b) any terms with a different prefix that are now maintained by that ontology. It does not contain any imports. It does, however, retain references to external ontologies within axioms as needed for definitions and reasoning. Such references, when displayed in Protege, will appear as identifiers only; that is, without labels. Finally, the base will have had reasoning already applied and will be stripped of redundant axioms. QUESTION: WILL THIS APPLY TO A SPECIFIC REASONER?
- full (REQUIRED; denoted by PURL ending with ONT-full.owl ): Content is as for base except that all referenced external terms are present (that is, imports are merged into the full release).
- other release artefacts (OPTIONAL; denoted by PURL ending with ONT-.owl): These include **non-classified**, **simple**, **basic**, and **simple-non-classified**. See the Release Artefacts link above for details on these.
- Every ontology MUST provide a ‘base’ release and MUST provide a ‘full’ release.

Communication Considerations

Link terms to issue tracker (tracker item) Any term (or set of terms) with an affiliated issue tracker item (term request or term discussion) SHOULD be linked to the relevant issue(s). Such linking SHOULD use the annotation property ‘term tracker item’ (IAO:0000233) and SHOULD NOT use a free text comment. The range for ‘term tracker item’ MUST consist solely of an IRI, without additional text, and the IRI MUST be for the issue tracker item.

Ontology Standardization Guidelines

Technical Considerations

Content Considerations

Release Considerations

Communication Considerations