KANBAN-838: Allow structured, post-composed phenotype annotations.#307
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KANBAN-838: Allow structured, post-composed phenotype annotations.#307
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This commit implements the proposition discussed in the Disease WG on
2025/10/29.
Briefly, it replaces the `phenotype_terms` slot of the
PhenotypeAnnotation class (which can only be used to describe a
phenotype using a list of phenotype terms) by a new slot tentatively
called `structured_phenotype_annotation_object`, which is expected to
hold an instance of a new class called `StructuredPhenotype`.
A StructuredPhenotype allows to describe a phenotype using a combination
of 4 types of ontological terms, in 4 distinct slots:
* terms from phenotype ontologies (`phenotype_terms` slot);
* terms from anatomical ontologies (`affected_location` slot);
* terms from developmental stages ontologies (`affected_stage` slot);
* additional terms ("qualifiers") from phenotype ontologies
(`qualifiers` slot).
gouttegd
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Superseded by #308, which proposes a better model that has been agreed upon in the Disease WG. |
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This PR tentatively implements the proposition discussed in the Disease WG on 2025/10/29.
Briefly, it replaces the phenotype_terms slot of the PhenotypeAnnotation class (which can only be used to describe a phenotype using a list of phenotype terms) by a new slot tentatively called structured_phenotype_annotation_object, which is expected to hold an instance of a new class called StructuredPhenotype.
A StructuredPhenotype allows to describe a phenotype using a combination of 4 types of ontological terms, in 4 distinct slots:
phenotype_termsslot);affected_locationslot);affected_stageslot);qualifiersslot).--
The PR currently does not address the need for arbitrary complex post-composed expressions, such as those seemingly used by ZFIN (e.g. https://zfin.org/action/ontology/term/ZFA:0000621#phenotype). The
StructuredPhenotypeclass could probably be extended to accommodate those, but this will require further discussion in the Disease WG.