Petab Yaml: Include petabId / modelId

[dlill]

Which problem would you like to address? Please describe. Reference the name of a petab estimation problem in its yaml file with a petabId or modelId field. Until now, the name of a petab is coded implicitly by the naming convention experimentalCondition_petabId.tsv, etc. In petab_select and potentially other applications we encounter a lot of different models, which might be derived from the same base petab. Therefore, having the petabId in the yaml would provide more flexibility in terms of renaming the tsv files (not necessary anymore) but still keeping the benefit of having a unique Id for each estimation problem

Describe the solution you would like Inlcude a field petabId in the yaml which accepts character inputs

Describe alternatives you have considered

Additional context We discussed this in the context of a petab_select meeting. I'm just putting it here so it's not forgotten

[dweindl]

Hi @dlill , thanks for your suggestion. We are currently preparing a proposal for allowing non-SBML models in PEtab, this will also include model IDs. More details in about 2 weeks.

[dweindl]

@dlill : Sorry for the delay. Would the changes proposed in https://github.com/PEtab-dev/PEtab/pull/538 address your needs? Specifically, that every model file gets an ID there.

[dlill]

Hey, I am currently moving out of the sysbio-field and will probably not work with petab anymore. But to quickly answer your question, with modelId I actually meant petabId, to enable referencing the petab problem itself by an ID. This would be helpful e.g. in model selection or also in visual comparisons of different models

petabId: myfancypetabId
format_version: 2.0.0
parameter_file: parameters.tsv
problems:
- condition_files:
  - conditions.tsv
  measurement_files:
  - measurements.tsv
  observable_files:
  - observables.tsv
  mapping_file: mappings.tsv # optional 
  models:
    id_for_model1:
      location: model1.xml
      language: sbml