Provenance

Minutes and task from the meetings

2025-09-29

• structure of ROCrate wrong (file references not relative to ro-create-metadata.json)

• parameter extraction script (based on file names parameter_...?)

• what is our dependency on an internet connection when running the script - dependency to external services?

• units

• version numbers of dependencies

• referencing of software (versions)

  • https://bioschemas.org/profiles/ComputationalTool/1.0-RELEASE
  • https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html
  • https://www.wikidata.org/wiki/Q14930378
  • https://obofoundry.org/ontology/swo.html

• howto link the benchmark (type) and the software/version (given as input to the workflow) to the processes - the current SPARQL query is not taking this into account?

• some vendors provide results with different "options", how do we handle that in the setup e.g. in the abaqus old verification manual

• can we get pdfs of the verification manuals of commercial tools, e.g. via NAFEMS?

• there is nextflow lineage in 25.04

• next steps

  • decision snakemake/nextflow follow both approaches in parallel? Discuss similarities between nextflow-prov and snakemake meta4ing plugins
  • other benchmarks / validation with exp. data (structure of that database)?
  • ROHub (testing) presentation next Thursday

2025-08-13

• Mahdi checks the github actions for his snakemake implementation in the nextflow branch

Links

• publish data at data.nfdi4ing.de oder https://www.re3data.org
• https://zenodo.org/records/13384262
• https://zenodo.org/records/11236871
• https://github.com/StroemPhi/dcat-4C-ap
• RO hub provides search functionality for ROCrates
  • and even a sparql endpoint, currently not publicly available but could be done
  • ROHub allows to enrich and add any annotation to the RO. You can use any standard vocabulary or a custom vocabulary to provide such annotations, i.e., what properties you will use to provide the values like ex:benchmarkType, ex:benchmarkDomain, etc.
  • How to add additional terms to the ROCrate is discussed here
  • maybe even include all the provenance information into a single ROCrate (rather than having a provenance.jsonld and a ro-crate-metadata.json
  • ROHub exposes a Restful API (swagger) – recommended for service integration
  • ROHub also provides python library (recommended for working with ROs). Please check tutorials
  • ROCrates offer the option of providing links to external resources via an embedded URL, so data could also be stored somewhere else and then only linked in the ROCrate
  • they provide a development environment for testing
• MathML is a standard for writing math equations, there is support from sympi to export that, but there is also a sbmlmath for doing the conversion in both directions
• SPARQL queries for workflow crates
• ROCrate validator