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Extend atlas names #1584

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merged 4 commits into from
Oct 14, 2024
Merged

Extend atlas names #1584

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3e9198c
Extend atlas names
arschat Oct 9, 2024
1c2ecfa
Fixed hca_tissue_atlas examples to match enum values
arschat Oct 9, 2024
2a9cfa9
Remove Eye - Other atlas name
arschat Oct 10, 2024
8e5eb3d
Ran release_prepare.py script.
arschat Oct 14, 2024
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2 changes: 1 addition & 1 deletion docs/jsonBrowser/module.md
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Original file line number Diff line number Diff line change
Expand Up @@ -365,7 +365,7 @@ Location: module/project/hca_bionetwork.json
Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
name | HCA Bionetwork the project is a part of (e.g. Kidney). | string | no | | Official HCA Bionetwork | Adipose, Breast, Development, Eye, Genetic Diversity, Gut, Heart, Immune, Kidney, Liver, Lung, Musculoskeletal, Nervous System, Oral & Craniofacial, Organoid, Pancreas, Reproduction, Skin | Kidney; Lung
hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). | string | no | | HCA Tissue Atlas | Blood, Retina, Lung, Kidney, Gut, Eye, Brain | Blood Atlas
hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). | string | no | | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, Eye - Other, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas Retina, Reproduction, Skin | Retina
hca_tissue_atlas_version | A field describing which version of the HCA Tissue Atlas is associated with the project (e.g. v1.0; v2.0) | string | no | | Official HCA Tissue Atlas Version | | v1.0; v2.0
atlas_project | A field describing if this project is the HCA Tissue Atlas project which integrates data from other datasets. | boolean | no | | Project Tissue Atlas Status | | Yes; No

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31 changes: 23 additions & 8 deletions json_schema/module/project/hca_bionetwork.json
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Expand Up @@ -48,17 +48,32 @@
"description": "A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). ",
"type": "string",
"enum": [
"Adipose",
"Blood",
"Retina",
"Lung",
"Kidney",
"Gut",
"Brain",
"Breast",
"Development",
"Eye",
"Brain"
],
"Eye - Other",
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You can remove "Eye - Other"; this will be refined as the atlas becomes more focused.

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Thank you, Dave! Done.

"GDN",
"Gut",
"Heart",
"Immune",
"Kidney",
"Liver",
"Lung",
"MSK",
"ORCF",
"Organoid-Endoderm",
"Organoid-Neural",
"Pancreas",
"Retina",
"Reproduction",
"Skin"
],
"user_friendly": "HCA Tissue Atlas",
"guidelines": "For example: Blood Atlas",
"example": "Blood Atlas"
"guidelines": "For example: Retina",
"example": "Retina"
},
"hca_tissue_atlas_version": {
"description": "A field describing which version of the HCA Tissue Atlas is associated with the project (e.g. v1.0; v2.0)",
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1 change: 1 addition & 0 deletions json_schema/update_log.csv
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@@ -1 +1,2 @@
Schema,Change type,Change message,Version,Date
module/project/hca_bionetwork,patch,Extend atlas names in hca_bionetwork,,
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@ESapenaVentura ESapenaVentura Oct 9, 2024 •
edited
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We should revisit what minor/patch updates are like. Thanks for following the guide https://github.com/HumanCellAtlas/metadata-schema/blob/master/docs/evolution.md#schema-versioning but I think extending an enumeration is not a patch change, as in my opinion any change in the schema that involves change in the validation rules should be at least a minor change. Anyways, this is good to go as per our specs! 🥇

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