OBOFoundry
Provide guidelines and quality control on consistent short ontology descriptions
Examining the description field https://obofoundry.org/ we see a variety of different lengths, styles
- An ontology for
- A controlled vocabulary for
- A structured controlled vocabulary for
- Standard terms for
- A community ontology for
- An integrated ontology for
- An ontological representation of
- An ontology for the standardization of terminology for ..
- FOO is an ontology for
- FOO (The Foo Obvious Ontology) is an ontology for
- FOO describes
-
This variance is potentially misleading, some users may be confused about the difference between "vocabulary" and "ontology" and think there is a meaningful difference when in fact the description is just reifying the start date of the ontology.
We should have a style guide for these, use consistent terminology, exclude adjectives that do not meaningfully separate ontologies ("integrated", "community", "structured", "formal", "standardized", "controlled" - these are all fuzzy, subjective, and ultimately meaning-free terms that all OBO ontologies should aspire to), keep meaningful adjectives ("upper", "application", taxonomic scope, etc).
We may want to keep the controlled vocabulary vs ontology distinction for the psi ontologies, since there is a meaningful difference in how these ontologies are expected to behave, but I think many of the ontologies that are currently described as vocabularies (primarily model organism ontologies) are as much ontologies as anything else
The ontology acronym or name should not be repeated in the description
After this, the descriptions vary wildly in conciseness, with some including random information about related projects, mini-essays, definitions of acronyms, parenthetical information, lists of other ontologies that are vaguely related or the ontology developer is friends with, ...
Sometimes species names are italicized, sometimes not.
We should have a style guide for the descriptions, this will help orient users who currently are presented with an overwhelming table and confusing descriptions. We should of course use reasonable judgment here - some ontologies such as OBI are a bit harder to concisely summarize than say an anatomy ontology, so some additional verbiage is useful and required.
I suggest the following template that allows for concise description of both content/scope and intended use:
- An [single optional meaningful adjective] ontology representing ... [, used for/in ....]
We can have templates for particular kinds of ontologies, for example:
Application ontologies:
-
An application ontology for [short description of purpose] covering [brief summary of contents]
Anatomy ontologies:
-
An ontology representing the (gross anatomy | gross anatomy and cell types | gross and cellular anatomy) [and life stages] of <Formal taxon name> [ (common name) ]
Avoid "development" to mean life stages
Related:
- #1966
If we do want to give guidance for this, we could add some guidance to the New Ontology issue template: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/.github/ISSUE_TEMPLATE/new-ontology.yml
Discussed during Ops call 2025-09-02. Overall there wasn't much concern about this, at least with respect to what's currently on the page. On the other hand, there was no objection to suggesting that, going forward, new ontologies follow the guidelines in whatever form they may take (and it's always possible that the maintainers of existing ontologies will revisit their descriptions to follow the guidelines).
Note that the following pertains to the 'short description' field in the ontology YAML file. Here is a straw man set of concrete guidelines that could be incorporated into a style guide page, with templates to follow.
The short description:
- SHOULD NOT include the ontology name or acronym (these are provided in separate fields).
- SHOULD NOT describe an ontology as a ‘controlled vocabulary’ or ‘terminology’ (and vice versa). That is, if the artefact is an ontology, describe it as such.
- SHOULD NOT include adjectives that do not meaningfully separate ontologies ("integrated", "community", "structured", "formal", "standardized", "controlled"), as these are all fuzzy, subjective, and ultimately meaning-free terms that would/should apply to all OBO ontologies.
- SHOULD NOT include random information about related projects or ontologies.
- SHOULD NOT include definitions of acronyms or other parenthetical information.
- SHOULD NOT use "development" to mean life stages.
- SHOULD keep meaningful descriptors (such as "upper", "application") and SHOULD include indication of taxonomic scope and ontology domain).
- SHOULD be concise as possible (preferably a single sentence).
- ??? (should or should not?) italicize species names.
Template ideas:
- "A(n) [single optional meaningful adjective] ontology representing ... [, used for/in ...]".
- For application ontologies: "An application ontology for [short description of purpose] covering [brief summary of contents]...".
- For anatomy ontologies: "An ontology representing the (gross anatomy | gross anatomy and cell types | gross and cellular anatomy) [and life stages] of <Formal taxon name> [ (common name) ]".
