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metadatacenter / cedar-terminology-server

A wrapper for the BioPortal API that simplifies the access to BioPortal ontologies, classes, value sets and values
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Allow Docker users to create value sets #29

Open martinjoconnor opened 6 years ago

martinjoconnor commented 6 years ago

Users who get BioPortal keys for use with CEDAR do not have the ability to create CEDAR value sets. Allow all BioPortal users do to this.

Related to: https://github.com/metadatacenter/cedar-project/issues/446

graybeal commented 6 years ago

hmmm. This would mean giving the world write access to the CEDAR value set ontology, and mixing all the value sets for all the CEDAR deployments in with the primary CEDAR system's value sets. So any CEDAR system would see all the CEDAR deployments' value sets.

And if those deployments wanted to manually curate their value sets someday, we'd have to let them manage it in CEDARVS.

This is an awkward deal, any way we look at it.

marcosmro commented 6 years ago

Note that the CEDAR Provisional Classes ontology (CEDARPC) is also affected by this issue.

martinjoconnor commented 6 years ago

Note that all CEDAR users currently have write access to the value set ontology.

Value set support in BioPortal is extremely limited at the moment. There is no way to delete value sets or even edit previously created value sets. So having external installations create value sets there would not really cause any additional issues (and would arguably encourage reuse) because they would not be able to modify existing resources. (What is also missing is fine-grained access to values sets -- instead authentication and authorization is at the level of the entire value set ontology. )

One could imagine allowing external deployments to create a new value set ontology if they wished to partition their value sets. Though - as Marcos just stated - if we are to do significant additional work with value sets we should likely completely rethink the current BioPortal implementation.