Review RO-Crate 1.1-DRAFT new sections

[stain]

Following discussion in call 2020-09-24 we will review RO-Crate 1.1-DRAFT until Thurs 2020-10-01, as we have added new sections that have not been proofread yet.

After review we aim to release 1.1 on Fri 2020-10-02.

From Changelog:

• Note: The RO-Crate metadata file is renamed to ro-crate-metadata.json to facilitate use of JSON editors. #82 #84
• Data entities can reference external resources with absolute URI #74
• Added section on considerations for Web-based Data Entities #74
• The root dataset is no longer required to be ./ #74
• RO-Crate Root directory no longer requires payload files #74
• Workflows and scripts section now aligned with BioSchemas ComputationalWorkflow profile #81
• Added section Programming with JSON-LD and note that @type might be an array #85
• Added new section Handling relative URI references #73
• JSON-LD context no longer sets @base: null #73
• Added note on Encoding file paths #77 #80
• Added section Choosing URLs for ad hoc terms #71 #90
• Section RO-Crate JSON-LD Media type expanded to suggest HTTP server configuration
• Update JSON-LD context to schema.org 10.0
• Remove HTML use of relatedLink property in RepositoryCollection example #91
• Distinguish between contextual/data entities #94
• Change theme to jekyll-rtd-theme and split into multiple pages #95

I merged #95 so you can navigate and edit the split files either from above or from https://www.researchobject.org/ro-crate/1.1-DRAFT/ - but note that "1.1-DRAFT" is missing from the left-hand menu before it is released. See Table of contents instead.

Volunteers per section:

• @dgarijo: Ad-Hoc vocabularies
• @dgarijo: Programming with JSON-LD
• @dgarijo: HTTP server configuration
• @dgarijo: (Workflows and scripts) - see also Reflect the MUST/SHOULD from BioSchemas profile #100
• @nsjuty: Workflows and scripts
• @nsjuty: Encoding file paths
• @ptsefton: Contextual vs Data Entities Attempt to distinguish contextual/data entities #94
• @ljgarcia: Handling relative URI references
• @ljgarcia: Web-based Data Entities
• @alaninmcr Workflows and scripts changes in Reflect the MUST/SHOULD from BioSchemas profile #100

Deadline: Thurs 2020-10-01

Either comment on this issue or make pull request/issue for changes.

[stain]

@dgarijo or @ljgarcia, are either of you able to also check out HTTP server configuration? At least the English, I tested each of the configs.

@nsjuty I added Encoding file paths as well.

@ljgarcia I added Web-based Data Entities as it's also about URI/identifiers.

[stain]

Also TODO for myself (or a volunteer that knows make/pandoc):

• @stain: Update Makefile to concatenate *.md in correct order
• @stain: Ensure concatenated HTML has correct internal #internal links or do a clever sed
• @stain: Make html/pdf for Zenodo (if above not possible, *zip of htmls)

[stain]

For Friday:

• @CaroleGoble and @stain: Draft press release (also add to Bioschemas website)

[alaninmcr]

To comply with the BioSchemas ComputationalWorkflow profile, the data entities MUST have the listed properties.

Better stated as: the data entities SHOULD comply with the BioSchemas ComputationalWorkflow profile. To comply with the profile, the data entities MUST ...

For FormalParameter, the data entities MUST describe the properties name, additionalType and encodingFormat.

[stain]

@alaninmcr if we are listing the MUSTs from the BioSchemas profiles then presumably we should also list the SHOULDs?

See my attempt in #100 - I am not sure if this can get a bit big and scary and people might think "Oh I won't do workflows in RO-Crate then" - or do you think it's OK?

[stain]

Thanks @nsjuty - merged #101 #102

[stain]

The so-called "clever sed" (bfd9b2f) actually worked and I fixed Makefile to make the Zenodo PDF again.

Preview of concatenated PDF: https://www.dropbox.com/s/4mtrw4xj4mz9xav/ro-crate-1.1.0-RC1.pdf?dl=0

[ljgarcia]

• Handling relative URI references review done, PR 104 created
• Web-based Data Entities review done, PR 103 created

[dgarijo]

Summary of my changes:

• @stain I went through Reflect the MUST/SHOULD from BioSchemas profile #100 and left a review there instead of creating a new PR
• I did a pull request with my review Review of Draft 1.1 #105 (not many changes were required, I also made sure that the examples using the new ro-terms ns are resolvable).