KANBAN-838: Allow structured, post-composed phenotype annotations.#306
Closed
gouttegd wants to merge 1 commit intoalliance-genome:mainfrom
gouttegd:new-phenotype-annotation-model
Closed
KANBAN-838: Allow structured, post-composed phenotype annotations.#306gouttegd wants to merge 1 commit intoalliance-genome:mainfrom gouttegd:new-phenotype-annotation-model
gouttegd wants to merge 1 commit intoalliance-genome:mainfrom
gouttegd:new-phenotype-annotation-model
Conversation
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).
chris-grove
changed the title
Contributor
Author
|
Superseded by #307, made from a local branch rather than a remote branch. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR tentatively implements the proposition discussed in the Disease WG on 2025/10/29.
Briefly, it replaces the
phenotype_termsslot of the PhenotypeAnnotation class (which can only be used to describe a phenotype using a list of phenotype terms) by a new slot tentatively calledstructured_phenotype_annotation_object, which is expected to hold an instance of a new class calledStructuredPhenotype.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/phenotype/statement/676864772, https://zfin.org/action/phenotype/statement/676876203). The
StructuredPhenotypeclass could probably be extended to accommodate those, but this will require further discussion in the Disease WG.