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Added collection_institute in specimen_from_organism.Fix#1606 #1607

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@arschat arschat commented Feb 11, 2025

Release notes

#1606

For specimen_from_organism.json schema:

  • Field name: collection_site
  • Field description: Institute where the biomaterial was collected on.
  • Field type: string
  • Required: no
  • Guidelines: Enter collection site latitude longitude in decimal degrees. If decimal degrees not available use site name or pseudonymized site name.

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  • Need 4 Reviewers to approve because this is a major update

@arschat arschat changed the title Added collection site in specimen_from_organism.Fix#1606 Added collection_site in specimen_from_organism.Fix#1606 Feb 28, 2025
"description": "Institute where the biomaterial was collected on.",
"type": "string",
"user_friendly": "Collection site",
"example": "52.175013, 0.141645; site_1; Addenbrooke's Hospital",
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These commas and semicolon are a bad smell. They represent separators that form a proprietary language (as in CS) to combine several values in one. JSON already has mechanisms for structuring data so why not use those.

This should be a module (a schema for a nested object) with three properties. Longitude, lattitude and name/description. That way you can express additional syntactical constraints on each of them and express their optionality/nullability.

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Thank you for your feedback. Created a module in a663ec1

@@ -117,6 +117,13 @@
}
]
},
"collection_site": {
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This sounds a lot like anatomical site. Is there a way to name this new property without that ambiguity?

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Thank you, changed to collection_institute in 28882ff

@arschat arschat changed the title Added collection_site in specimen_from_organism.Fix#1606 Added collection_institute in specimen_from_organism.Fix#1606 Mar 3, 2025
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4 participants