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.

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

Add altname or preferred variable name field to entities.yaml in schema #585

Closed
tsalo opened this issue Aug 28, 2020 · 3 comments · Fixed by #616
Closed

Add altname or preferred variable name field to entities.yaml in schema #585

tsalo opened this issue Aug 28, 2020 · 3 comments · Fixed by #616
Labels
infrastructure schema Issues related to the YAML schema representation of the specification. Patch version release.

Comments

@tsalo
Copy link
Member

tsalo commented Aug 28, 2020

This new field would specify the preferred variable name by which the entities are referred in other tools, like pybids. One example is the ce entity. The full name for the entity is "Contrast enhancing agent", the entity itself is ce, and the pybids variable is ceagent. To specify the preferred variable name (or shortened name) would make tools that use the schema more useable to outsiders.

The exact variable names could be taken directly from pybids at this point. I don't know if any other elements to the specification need this field, so please let me know if I'm missing something.

This came up in today's NIDM-Terms call. Tagging @jbpoline, @satra, and @yarikoptic.

EDIT: Perhaps a top-level YAML file should be added that describes the other YAML files/folders, in which case we have the YAML file/folder name (e.g., datatypes), the actual name ("Data type"), and some preferred variable name, as used in tools like pybids (datatype).

@effigies
Copy link
Collaborator

The rule we came up with for PyBIDS was that the entity's queryable name should have the entity key as an initial substring, and within that constraint it should be as readable as possible.

bids-standard/pybids#489 (comment)

@tsalo
Copy link
Member Author

tsalo commented Aug 28, 2020

To be honest, the only one that's not easily inferred at the moment is ceagent, although I get why you didn't go with contrast. In the rest of the cases, I think we could just grab the first word in the entity name. Still, I think moving that field (and naming logic) here would be good.

@sappelhoff
Copy link
Member

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
infrastructure schema Issues related to the YAML schema representation of the specification. Patch version release.
Projects
3 participants