Each term should have a natural language description

[paulmillar]

This issue was triggered by the question: does PaNET itself provide a precise and authoritative definition of the meaning of a PaNET term? If PaNET is authoritative, then I believe the terms should be defined in PaNET without relying on any external definitions.

There are two OBO annotations being used in this context: obo:IAO_0000115 and obo:IAO_0000119.

The annotation obo:IAO_0000115 ("definition") has the following editor note:

2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.

The annotation obo:IAO_0000119 ("definition source") has the following editor note:

Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007

Currently, there are some 94 terms that use obo:IAO_0000119 ("definition source") to point to a Wikipedia entry. To me, linking to Wikipedia with obo:IAO_0000119 semantics delegates responsibility for defining the term to Wikipeda. In other words, for these terms, PaNET is not authoritative but rather Wikipedia is.

In contrast, there are eight terms that are annotated with obo:IAO_0000115 ("definition") and a natural language description. For these terms, PaNET is authoritative.

One term (PaNET01025) uses both obo:IAO_0000115 and obo:IAO_0000119, which is somewhat confusing, but I would take to mean the definition comes from Wikipedia.

During the 2023-11-02 PaNET maintenance meeting, there seemed to be broad support for the idea that PaNET is authoritative.

If the first para is accepted and if we want PaNET to be authoritative then each term must contain a natural language definition that is independent of any other source.

Just to be clear, we can still includes Wikipedia pages (or, perhaps better, Wikidata links) as related terms (equivalent terms, broader terms, etc). This would enable semantic cross-walking, etc.

[gkoum]

An ontology does not have to be authoritative but then we have to make sure that our referred definitions are stable and persisted as well as semantically equal to what our ontology structure implies.This seems more difficult than including a definition using IAO_0000115 but scientists can verify that.

In cases where we specify both obo:IAO_0000119 and obo:IAO_0000115 I would say that our definition is stronger but we also give a source where more information can be retrieved although we can use other terms for that and avoid having them both.