Finalize proposal submission

[cmaumet]

• First pass at updating the BEP028 spec to be compliant with latest discussions.

Add a usage examples of this spec for the following:

• 1- simplest model with one activity and its parameters,
• 2- workflow with more than 1 activity,
• 3- encoding environement (Matlab, docker, bash, etc.).
• 4- an example with hierarchies of activities (use isPartOf form PROVONE)
• 5- an example that uses the ontology of processings / image types
• 6- an example discussing file-level prov VS dataset-level prov

[remiadon]

@cmaumet I just updated the document, mainly to

1. update the examples (json-ld files structure and content)
2. discuss about dataset-level representation (global sidecar file) VS file-level representation (one sidecar file per datafile)

IMO point 2 is not really to be discussed, as we strive for a global sidecar file in most cases, and even allow definitions to be shared across multiple files.

Should would start a separate thread to add more examples and usecases for beta users of BIDS-prov ??
There is a running issue that may be suited for this, here #56

[remiadon]

TODO : add this field to the common definition, just after @context

"BIDSProvVersion": "1.0.0",

[cmaumet]

@remiadon: you can implement the changes to the examples (version) directly in your PR #58.

[remiadon]

@cmaumet done in 47fb0a9

BTW is there a way to define a common header for all sides car files ??
Just adding "BIDSProvVersion": "1.0.0", got me going into editing all the .json files in our repo