Provenance

Minutes and task from the meetings

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}(https://pypi.org/project/sbmlmath/) for doing the conversion in both directions