Deprecate EnvironmentalMaterialTerm, Pathway
#222
Conversation
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mslarae13
requested review from
naglepuff,
aclum,
kheal,
SamuelPurvine,
sujaypatil96,
turbomam,
brynnz22 and
eecavanna
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I like the PR title! It tells me what will happen on the destination branch if these changes were to be merged into it. |
src/schema/annotation.yaml
Outdated
| @@ -110,6 +112,7 @@ classes: | |||
| - KEGG.ORTHOLOGY prefix is used for KO numbers | |||
| todos: | |||
| - is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable in the Data Portal? | |||
| deprecated: "not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881" | |||
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We do use the KEGG prefix the both of the aggregation tables which is I think an argument for keeping OrthologyGroup which would also mean keeping FunctionalAnnotationTerm.
i think what should happen is the range of gene_function_id should be OrthologyGroup plus a structured_pattern.syntax constraint @turbomam
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@SamuelPurvine this is what we were talking about on Wednesday, yes?
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Yep, and is why I'd brought it up :)
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@aclum @SamuelPurvine @mslarae13
Making sure I understand various conversations - if you will have a use for OrthologyGroup and parent classes, I should close this PR without merging, leave the classes in the schema, and they will be used after berkeley rollout when you make changes to gene_function_id?
bmeluch
changed the title
EnvironmentalMaterialTerm, FunctionalAnnotationTerm + childrenEnvironmentalMaterialTerm, Pathway
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I removed the deprecation for |
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That'll be a @aclum thing :) |
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Approved this PR. |
See microbiomedata#1881
This PR is the first step in deprecating
EnvironmentalMaterialTerm,FunctionalAnnotationTerm+ children. It adds adeprecated:string to each class definition. This PR will need to be reviewed to see if/when it can be merged in during the Berkeley schema rollout, or if we need to wait.