Provenance

Minutes and task from the meetings

2025-09-16

version numbers of dependencies and internet connection required?
referencing of software (versions)
howto link the benchmark (type) and the software/version (given as input to the workflow) to the processes?
units
parameter extraction script (based on file names?)
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?
snakemake/nextflow follow both approaches in parallel? Discuss similarities between nextflow-prov and snakemake meta4ing plugins

2025-08-13

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

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