Create SED-ML files for Physiome projects that don't have them and annotate that these were computationally-generated from CellML files
jonrkarr opened this issue · 0 comments
jonrkarr commented
- Determine which are top-level CellML files
- Use code below to generate a SED-ML file for each top-level CellML file
- Add metadata to indicate that each SED-ML file was computationally-generated from a CellML file
- Package everything into a COMBINE archive
Code to generate SED-ML from CellML
See
https://github.com/biosimulators/Biosimulators_utils/blob/c99d27c32bf4deb5b0348e5fb8470de5e88b7904/biosimulators_utils/model_lang/cellml/utils.py#L25
https://github.com/biosimulators/Biosimulators_utils/blob/c99d27c32bf4deb5b0348e5fb8470de5e88b7904/biosimulators_utils/__main__.py#L122
Metadata to annotate that files were computationally generated
Triple
- Subject: OMEX library URI for SED-ML file (e.g.,
http://omex-library.org/BioSim0001.omex/simulation.sedml
) - Predicate:
http://biomodels.net/model-qualifiers/isDerivedFrom
- Object: OMEX library URI for source CellML file (e.g.,
http://omex-library.org/BioSim0001.omex/model.cellml
)
RDF-XML example
<rdf:Description rdf:about="http://omex-library.org/BioSim0001.omex/simulation.sedml">
<bqmodel:isDerivedFrom>
<rdf:Description>
<dc:identifier rdf:resource="http://omex-library.org/BioSim0001.omex/model.cellml"/>
<rdfs:label>model</rdfs:label>
</rdf:Description>
</bqmodel:isDerivedFrom>
</rdf:Description>