Add URIs for external resources / ontologies

[rly]

Currently, with the new ExternalResources data type, each term is associated with an external resource (e.g., ontology), a unique identifier at the resource, and the URI for the resource entity.

Users would also like to associate a URI for the external resource. For example, the external resource "NCBITaxon" would have the URI "https://www.ncbi.nlm.nih.gov/taxonomy" associated with it. To normalize these data in the "resources" table, we should add a new table with fields (name, uri) and change the "resource_name" field in the "resources" table to be an index (foreign key) into the new table.

This change requires further feedback and coordination with ontology users.

[rly]

@ajtritt @oruebel Should we include this change and release hdmf-common-schema 1.3.0 or hold this off until a later release?

[ajtritt]

We'll need to include it. The hdmf code will need these types defined in the schema, otherwise TypeMap.register_class will choke.

[rly]

To be clear, I mean, should we include the addition of an additional URI for the resource, on top of everything that has already been implemented in HDMF and set in hdmf-common-schema. AFAIK, the proposed change has not yet been implemented in either the schema or HDMF.

[ajtritt]

To be clear, I mean, should we include the addition of an additional URI for the resource,

oops... didn't read the issue in detail. This might take some time to add. If we need to make a release, then I suggest not letting this hold it up

[oruebel]

Since this is still in development, I don't think it will be an issue to add this later in another release.

[rly]

Great, thanks for the input.

[oruebel]

1. Change the name of theResourceTable to EntityTable
2. Add ResourceTable with columns id, name, and uri to describe the resources
3. Change recource_name column in the ResourceTable to resource_id to point to the new ResourceTable
4. Update tests for EntityTable and add tests for ResourceTable. See https://github.com/hdmf-dev/hdmf/blob/dev/tests/unit/common/test_resources.py
5. Write documentation describing the structure for managing ExternalResources See https://github.com/hdmf-dev/hdmf/tree/dev/docs/source
6. Write documentation describing the use of ExternalResources See https://github.com/hdmf-dev/hdmf/tree/dev/docs/source

[rly]

The schema parts of this issue have been resolved by #49.

[oruebel]

@rly @mavaylon1 has this issue been completed?

[rly]

This is done.