Update data dictionary generation process #1

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opened 2024-09-27 08:27:52 +00:00 by jsheunis · 0 comments

jsheunis commented

2024-09-27 08:27:52 +00:00

(Migrated from hub.datalad.org)

The background: https://hub.datalad.org/datalink/org/issues/3

The current state: https://hub.datalad.org/datalink/org/issues/3

During discussion with @mih, the following points were made:

The current approach (adding neurobagel annotations to an existing LinkML schema) requires an understanding of LinkML internals for a maintainer to be able to create/update a data dictionary, ideally this should not be a requirement.
In this comment I mentioned:

I started out with inspecting the neurobagel data dictionary jsonschema, then created a LinkML schema for it: https://github.com/jsheunis/datalad-concepts/blob/neurobagel/src/nbdd/unreleased.yaml

This schema is now located in the current repository under https://hub.datalad.org/datalink/tools/src/branch/main/schemas/nbdd/unreleased.yaml. Generating shacl shapes from this schema and subsequently generating a shacl-vue form could be an appropriate alternative to the current way of generating a data dictionary. The maintainer would have to use the form to construct the data dictionary and then download it once.
Another alternative could be to use the current approach of embedding the Neurobagel-required info into the LinkML schema, but in a more logical way using existing concepts rather than a string-encoded annotation. The dlco already has classes for a dlthing:Property and a dlthing:QuantitativeProperty that could be used in an improved approach to generate a Neurobagel data dictionary from a dlco-based schema. The exact link of these with neurobagel terms and how this would influence implementation are still a bit hazy to me.

The first question is: do we want a maintainer to fill in a form or to update a LinkML schema in order to generate the data dictionary?

The background: https://hub.datalad.org/datalink/org/issues/3 The current state: [https://hub.datalad.org/datalink/org/issues/3](https://hub.datalad.org/datalink/tools#generating-a-data-dictionary-for-neurobagel-https-neurobagel-org-from-a-linkml-schema) During discussion with @mih, the following points were made: - The current approach (adding neurobagel annotations to an existing LinkML schema) requires an understanding of LinkML internals for a maintainer to be able to create/update a data dictionary, ideally this should not be a requirement. - In [this comment](https://hub.datalad.org/datalink/org/issues/3#issuecomment-68) I mentioned: > I started out with inspecting the neurobagel data dictionary jsonschema, then created a LinkML schema for it: https://github.com/jsheunis/datalad-concepts/blob/neurobagel/src/nbdd/unreleased.yaml This schema is now located in the current repository under https://hub.datalad.org/datalink/tools/src/branch/main/schemas/nbdd/unreleased.yaml. Generating shacl shapes from this schema and subsequently generating a `shacl-vue` form could be an appropriate alternative to the current way of generating a data dictionary. The maintainer would have to use the form to construct the data dictionary and then download it once. - Another alternative could be to use the current approach of embedding the Neurobagel-required info into the LinkML schema, but in a more logical way using existing concepts rather than a string-encoded annotation. The `dlco` already has classes for a [`dlthing:Property`](https://github.com/psychoinformatics-de/datalad-concepts/blob/8ef7b6c46777669188f6a1e7273a35ff5ea1e497/src/thing/unreleased.yaml#L315) and a [`dlthing:QuantitativeProperty`](https://github.com/psychoinformatics-de/datalad-concepts/blob/8ef7b6c46777669188f6a1e7273a35ff5ea1e497/src/thing/unreleased.yaml#L326) that could be used in an improved approach to generate a Neurobagel data dictionary from a `dlco`-based schema. The exact link of these with neurobagel terms and how this would influence implementation are still a bit hazy to me. The first question is: do we want a maintainer to fill in a form or to update a LinkML schema in order to generate the data dictionary?