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Provenance
2025-09-29
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structure of ROCrate wrong (file references not relative to ro-create-metadata.json)
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parameter extraction script (based on file names parameter_...?)
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what is our dependency on an internet connection when running the script - dependency to external services?
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units
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version numbers of dependencies
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referencing of software (versions)
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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?
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some vendors provide results with different "options", how do we handle that in the setup e.g. in the abaqus old verification manual
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can we get pdfs of the verification manuals of commercial tools, e.g. via NAFEMS?
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there is nextflow lineage in 25.04
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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
- 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
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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