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

Adding identifer namespaces? #1354

Open
gdower opened this issue Sep 16, 2024 · 4 comments
Open

Adding identifer namespaces? #1354

gdower opened this issue Sep 16, 2024 · 4 comments

Comments

@gdower
Copy link
Contributor

gdower commented Sep 16, 2024

In the xrelease, I see ZooBank identifiers like this:

local:d8167df7-42af-4dd2-bc49-5aae7f11a500
https://api.checklistbank.org/dataset/301904/nameusage/DV3JP

It seems like it should be prefixed with their lsid namespace instead of local:?

urn:lsid:zoobank.org:act:D8167DF7-42AF-4DD2-BC49-5AAE7F11A500
https://zoobank.org/NomenclaturalActs/d8167df7-42af-4dd2-bc49-5aae7f11a500

As far as I can tell, the local: namespace gets added by the backend:

https://www.checklistbank.org/dataset/2037/verbatim?q=D8167DF7-42AF-4DD2-BC49-5AAE7F11A500

I might also start using COLDP alternativeID for Systema Dipterorum in order to add the ZooBank IDs soon, although Systema Dipterorum is in the process of adding the ZooBank IDs.

@mdoering
Copy link
Member

Yes, the local namespace isn't great. It happens during import of ZooBank though, not in the XRelease which just copies them over. Here is the source record:
https://api.checklistbank.org/dataset/2037/taxon/d8167df7-42af-4dd2-bc49-5aae7f11a500

Which is based on this verbatim record:
https://www.checklistbank.org/dataset/2037/verbatim/242319

For the XRelease I would think removing local identifiers makes sense and making sure that nomenclator identifiers are added with their proper namespace.

@mdoering
Copy link
Member

Unless ZooBank shares a different dwca I don't know how to improve this. The scientificNameID is taken as an alternative name id, but there is no scope. I could maybe block it from alt ids in case the name has the exact same identifier like we have here

@gdower
Copy link
Contributor Author

gdower commented Sep 19, 2024

So the dwca:ID needs their urn:lsid:zoobank.org:act: namespace added onto it or else it gets namespaced as local: by the clb importer? Or should they be putting the namespace on all of their IDs like WoRMS?

https://api.checklistbank.org/dataset/2037/verbatim?q=d8167df7-42af-4dd2-bc49-5aae7f11a500

Is that what the identifier without scope issue means?

Perhaps having a dataset configuration option for ID namespace would be useful (like the dataset option for adding extinct to all values?). Then for alternativeID in other datasets, we'd always need to put the namespace especially if its not the dataset's namespace.

@mdoering
Copy link
Member

yes, identifier without scope means that it is just a local id.
dwca:ID is not the source of the problem though, it is dwc:scientificNameID or in ColDP it is the coldp:alternativeID fields. The main IDs are expected to be local.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants