Purpose

This is an ontology to annotate omnibenchmark runs.

We provide three components:

the ontology formalization (turtle)
an example knowledgebase (turtle) with a simplified setup:
- one data module
- two filtering modules
- one method module, run with different parameters
another (more realistic) example, the the iris-example knowledgebase somewhat resembling the omnibenchmark named iris-example
some SPARQL queries, including:
- get_deliverables_by_activity.sparql
- get_deliverables_by_epoch.sparql
- get_deliverables.sparql
- get_file_provenances_one_hop.sparql
- get_file_provenances_recursive.sparql
- get_modules.sparql

To generate these triples and send them to the endpoint: adopt and reuse epoch.py from omni-cli (it's mainly python native templating).

Design philosophy

Keep it deliverable-centric (file-centric), because bioinformatics workflows typically are.
Reduce overlaps to renku's ontology but keep in mind future cross-queries; we can add federated queries and/or merge graphs by matching literals (i.e. plan ids or activity ids).
Make use of gitLFS / S3 buckets identifiers, to streamline dataset retrieval in a renku-free manner.
Make use of module names and file names, to perhaps switch to renku-free command-line workflows at some point.
Keep versions/epochs explicit.

Layout generated by WebVOWL 1.1.7.

Missing git hook/populate the endpoint on push
To be linked to the container/codebase tagging/branching system
(Sept 2023) Renku's named key:value parameters are named parameterMaps and only apply to composite plans, not to plans: source
renkulab API queries (to potentially replace with our custom queries)