Use canonical Bioschemas prefix

[fbacall]

From reading a discussion here: BioSchemas/specifications#653 (comment)

It seems there was a conclusion to use https://bioschemas.org/terms/ as the prefix for Bioschemas' own types/properties.

The Bioschemas term mappings in the RO-Crate context should be updated:

"ComputationalWorkflow" : "https://bioschemas.org/terms/ComputationalWorkflow"
"input" : "https://bioschemas.org/terms/input"
"output" : "https://bioschemas.org/terms/output"
"FormalParameter" : "https://bioschemas.org/terms/FormalParameter"

[elichad]

CodeMeta are also establishing canonical URIs: codemeta/codemeta#468

Proposing for discussion with the steering committee: whether we should update these URIs now (in a minor/patch release) or wait for v2.0

[stain]

No formal decision from steering commtitee. But if we considered the wrong bioschemas context a bug, then it might match for a patch update. RO-Crate 1.1.3 had an update to fix the mapping from RepositoryObject to http://pcdm.org/2016/04/18/models#Object

[elichad]

For the CodeMeta side, their URI update will be part of CodeMeta v4 (not yet released and don't know the timeline for this) (see codemeta/codemeta#360 for versioning discussion). Currently the RO-Crate 1.2 context is explicitly based on CodeMeta v3.0. So updating the CodeMeta URIs would probably take us to 1.3 IMO.

The Bioschemas terms are not versioned in the same way so I think we can consider them separately and sooner (I'm more inclined to consider the interim terms a "bug" and do a patch release).

[elichad]

Discussed in community call 2026-04-09.

@simleo highlighted that this change would have significant implications for the SHACL-based validator - as it utilises these URIs for validating the presence and value of these terms. If we released an updated 1.2.1 context, some versions of the validator would cease to work as intended (because they are manually programmed with the URIs used in the 1.2.0 release).

There might also be other RO-Crate users who depend on the RDF representation of crates which use these terms and would be caught off guard by a change in the URIs.

Therefore, even though this is a very minor change in the grand scheme of the spec, I have changed my mind - I suggest we make a 1.3 release which updates these URIs, but is otherwise exactly the same as 1.2. The majority of users can use either 1.2 or 1.3 with no real difference, but users who are specifically working with workflows and workflow run crates should use 1.3 (and we can mandate this in the relevant profiles).

The other option suggested in the call was that the Workflow/Workflow Run profiles could override these terms in their contexts. But that seems like a messy solution that could cause new issues (e.g. which context will automated tools prioritize?).

cc @ResearchObject/steering-committee - further opinions welcome