Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level #1603

Merged
merged 7 commits into from
Sep 11, 2023
Merged

[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level #1603

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
f046e99
update level description
Remi-Gau Aug 29, 2023
70f0d77
Merge branch 'master' into enh/object_for_levels
Remi-Gau Aug 29, 2023
b2f8ad4
Apply suggestions from code review
Remi-Gau Aug 29, 2023
2e987ec
add link to glossary
Remi-Gau Sep 6, 2023
5637743
rm weird file
Remi-Gau Sep 6, 2023
1f8d3f9
fix path
Remi-Gau Sep 6, 2023
c1da9bb
Merge branch 'master' into enh/object_for_levels
Remi-Gau Sep 6, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions src/common-principles.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -513,6 +513,29 @@ Example:
}
```

Each level can be described with a string as in the example above,
or with an object containing the fields [`Description`](./glossary.md#description-metadata)
and [`TermURL`](./glossary.md#termurl-metadata)
like in the example below.

```JSON
{
"sex": {
"Description": "sex of the participant as reported by the participant",
"Levels": {
"M": {
"Description": "Male",
"TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68008297"
},
"F": {
"Description": "Female",
"TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68005260"
},
}
}
}
```

### Key-value files (dictionaries)

JavaScript Object Notation (JSON) files MUST be used for storing key-value
Expand Down
5 changes: 3 additions & 2 deletions src/schema/objects/metadata.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3371,9 +3371,10 @@ TermURL:
name: TermURL
display_name: TermURL
description: |
URL pointing to a formal definition of this type of data in an ontology
available on the web.
URL pointing to a formal definition of this type of data in an ontology available on the web.
For example: https://www.ncbi.nlm.nih.gov/mesh/68008297 for "male".
type: string
format: uri
TimeZero:
name: TimeZero
display_name: Time Zero
Expand Down