Allow using similarity_measure at the set level.
#412
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We add the `similarity_measure` slot to the MappingSet class, as a propagatable slot. It should be quite common that all `similarity_score` for all mappings in a set are determined using the same measure, so it makes sense to allow setting the measure once and for all at the set level, without having to repeat that information for all individual mappings. closes #411
matentzn
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Feb 24, 2025
Propagatable slots must be declared as instantiating the sssom:Propagatable interface to be properly marked as propagatable.
matentzn
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Feb 24, 2025
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I tested a schema build, and it all works as intended.
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gouttegd
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- [x] `docs/` have been added/updated if necessary - [x] `make test` has been run locally - ~~[ ] tests have been added/updated (if applicable)~~ - ~~[ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/master/CHANGELOG.md) has been updated.~~ Already covered by previous changes The `added_in` annotation is used to indicate that a slot has been introduced in a specific version of the specification. For now, that annotation is only used in the model-wide definition of slots, which means it can only indicate when a brand new slot has been introduced – it can not be used to indicate that a pre-existing slot has been added to a class in which it was not used before. For example, the `similarity_measure` slot has existed since before 1.0, but has been only been added to the `MappingSet` class for version 1.1. Currently that information is _not_ contained in the model, implementers need to check the [Model changes across versions](https://mapping-commons.github.io/sssom/spec-model/#model-changes-across-versions) section of the spec to be aware of that. Likewise for `curation_rule` and `curation_rule_text`, which have just been added to the `MappingSet` class. In this PR, we make use of LinkML's `slot_usage` mechanism to add the `added_in` annotation not only to the general (model-wide) definition of a slot, but also to the specific instance of a slot within a class. This allows to encode, directly into the model, that the use of `similarity_measure`, `curation_rule`, and `curation_rule_text` at the level of the `MappingSet` class is only possible starting from version 1.1. (This really should have been done directly in the PRs that added those slots to the `MappingSet` class – #412 and #472 –, but at the time I had not realized that it was possible to use `slot_usage` to add annotations to a slot only within the context of a particular class.)
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Resolves [#411]
docs/have been added/updated if necessarymake testhas been run locally[ ] tests have been added/updated (if applicable)If you are proposing a change to the SSSOM metadata model, you must
[ ] provide a full, working and valid example inexamples/[ ] provide a link to the related GitHub issue in thesee_alsofield of the linkml model[ ] provide a link to a valid example in thesee_alsofield of the linkml modelThis PR adds the
similarity_measureslot to theMappingSetclass, as a propagatable slot. It should be quite common that allsimilarity_scorefor all mappings in a set are determined using the same measure, so it makes sense to allow setting the measure once and for all at the set level, without having to repeat that information for all individual mappings.