Create SED-ML files for Physiome projects that don't have them and annotate that these were computationally-generated from CellML files - Githubissues

biosimulations / biosimulations-physiome

Command-line application for publishing the Physiome model repository of physiological models to the BioSimulations repository for simulation projects

https://docs.biosimulations.org/repositories/physiome

0 stars 0 forks source link

Create SED-ML files for Physiome projects that don't have them and annotate that these were computationally-generated from CellML files #10

Closed jonrkarr closed 2 years ago

jonrkarr commented 2 years ago

[x] Determine which are top-level CellML files
[x] Use code below to generate a SED-ML file for each top-level CellML file
[x] Add metadata to indicate that each SED-ML file was computationally-generated from a CellML file
[x] 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>