Is DNA a preparation? - Githubissues

DINA-Web / dina-model-concepts

Repository containing information to define data model boundaries

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Is DNA a preparation? #31

Closed cgendreau closed 3 years ago

cgendreau commented 5 years ago

From @jmacklin : Is DNA a preparation? It is sampled from an object and then is either a preparation that is destroyed or a preparation that is a tube stored in a freezer. Makes sense as you would need to sub-sample from the tube to do another analysis. Support Biobanking.

cgendreau commented 5 years ago

According to the current definition of Preparation: Process used to move from Material Sample to Catalogued Object.

I think it should be changed to avoid confusion with DNA preparation.

This is how I see DNA preparation (at the moment):

MaterialSample --[Preparation] --> CataloguedObject --[Preparation from the previous preparation] --> Sample (DNA extraction).

It would also allow to add determination(s) since we link determinations to Catalogued Object. But if we do it that way, I think there is no real purpose for sourceMaterialSample.

cgendreau commented 5 years ago

I would suggest to make the following changes:

Preparation definition should be changed to:

Process initially used to move from Material Sample to Catalogued Object. The process can then be repeated from a previous preparation.

Remove sourceMaterialSample from the proposed data model

@ssbilkhu you agree?

falkogloeckler commented 3 years ago

As of discussion in issue #45

we only define preparation processes
preparation processes can be destructive, so a physical (sub-)entity is taken from a physical entity that could lead to a catalogued object or not
DNA sampling is a preparation process
DNA sample is a physical entity that could be consumed after analyses or could be accessioned in a biobank. So it could become a catalogued object.

@jmacklin & all: If you agree with the summary this issue can be closed

jmacklin commented 3 years ago

Agreed!

cgendreau commented 3 years ago

Do we have it explicitly explained in the information model?

falkogloeckler commented 3 years ago

Do we have it explicitly explained in the information model?

We don't, but implicitly it is covered. However, I addressed DNA sampling as an example now. See patch: https://github.com/DINA-Web/dina-model-concepts/pull/51

cgendreau commented 3 years ago

Merged the PR and closing the issue since we all agree.