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Update bioschemas citations #187

Merged
merged 4 commits into from
Jan 24, 2022
Merged

Update bioschemas citations #187

merged 4 commits into from
Jan 24, 2022

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stain
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@stain stain commented Jan 20, 2022

Refer to BioSchemas 1.0-RELEASE versions without / in their @id URIs. Example:

{ "@id": "workflow/alignment.knime",  
  "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
  "conformsTo": 
      {"@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE"},
  "input": [  {"@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b"} ]
},
{
  "@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b",
  "@type": "FormalParameter",
  "conformsTo": 
    {"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"},
  "..": ""
}

This fixes issue #185

This also removes the early attempt of sdConformsTo structure from #154 and adds a footnote:

This is a liberal interpretation of conformsTo as it is the structured data about the workflow (this JSON-LD object) that conforms to the ComputationalWorkflow profile, not the file content of a workflow data entity (workflow/alignment.knime). Instead of introducing a sdConformsTo similar to sdPublisher, we here follow the current Bioschemas convention of indicating profile conformance when the JSON-LD is embedded within HTML pages.

Discussion in schemaorg/schemaorg#1516 schemaorg/schemaorg#2887 seems to suggest a structuredData property to another blank node entity about the metadata itself, which could then have its own creator, etc. (and in our case conformsTo). My view now is that adding a nested structuredData contextual entity in RO-Crate will get excessively verbose (particularly on the FormalParameter which is already a #nonDownloadable contextual entity).

This fixes issue #185

TODO: Resolve sdConformsto from #154 to align with
schemaorg/schemaorg#1516
schemaorg/schemaorg#2887

Adding a nested structuredData contextual entity here will get
excessively verbose (particularly on the FormalParameter which is
already a #nonDownloadable contextual entity)
@stain stain merged commit 7f7ce21 into master Jan 24, 2022
@stain stain deleted the update-bioschemas branch January 24, 2022 14:47
@stain stain added this to the RO-Crate 1.2 milestone Mar 23, 2023
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