Add proposed ontology for BIDSprov

[neurorepro]

This PR is to propose an extension of the current BIDS prov specifications with an ontology anticipating the use of prospective provenance in addition of the retrospective aspect BIDS prov focused on. It is an ontology:

• including both prospective and retrospective provenance
• allowing for sorted lists, especially useful for program arguments in prospective aspect
• privileging reuse of existing ontologies, notably:
  • prov in particular provone and provo for provenance
  • sd (software description ontology) for software description, mostly used in prospective aspect
  • co (collections ontology) for OWL-DL compatible ontology of sorted lists
• adding new classes / properties when (subjective) it adds useful features and/or significantly clarity, such as:
  • combining sorted lists of the collections ontology with the prov key-val pairs to create sorted list of key-val pairs, particularly useful to describe program parameters (prospective aspect)
  • simplifying potentially complex port concepts in prov based on reification by using instead direct hasInput hasOuput properties
  • removing anonymous classes / reification when possible (e.g. qualifiedGeneration, qualifiedGeneration, qualifiedUsage)
  • adding a direct correspondence between prospective and restrospective aspects with e.g. hasInput and hasOutput prospective properties matching the hadInput and hadOuput retrospective properties
    • This is in line with ontologies focusing on both prospective and retrospective typically do not use provone but rely on wf4ever (cf e.g. taverna model attached) for better correspondence between prospective and retrospective terminology
• optimizing ontology matching
  • the hadInput and hadOuput new properties were defined as subproperties of used and wasGeneratedBy, which can be recovered as parent properties thanks to the OWL-DL legal ontology
• featuring many entities / properties specific to programs as typically used in neuroimaging (and other field) workflows:
  • program version
  • program source code
  • container image
  • etc.

Future changes will include adding in the retrospective aspect more mirror properties present in the prospective worlfow description.

The suggested ontology has been implemented to describe both prospectively and retrospectively a workflow including the bet and flirt tools, keeping in mind that mostly (only?) the retrospective aspect would be relevant for BIDS prov

CONCISE ontology

PROVONE ontology

TAVERNA ontolog

y

[cmaumet]

(Note for @bclenet: let's keep this PR open as it is as this is work-in-progress)