search

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

Open Issue regarding incorrect CellML schema #53

Closed bilalshaikh42 closed 2 years ago

bilalshaikh42 commented 2 years ago

Many of the errors in the models are due to the attribute "id" being present in the equation element, which is flagged by the schema as incorrect. However, the CellML primer explicitly mentions that this is expected use. https://www.cellml.org/getting-started/cellml-primer

Often it is useful to be able to identify a particular mathematical equation with a reference ID. For example, this ID could be the original equation number taken from the published paper to designate the same equation in the code. Alternatively, an equation ID could also be helpful during the process of model validation, allowing the quick identification of a possible error in the code. IDs are assigned to math elements rather than to the equations themselves (as shown in the fragment of CellML code below); it can therefore be useful to allocate one math element per equation to allow equations to be identified by their ID.

Therefore the schema used in this package, which is taken directly from the CellML page, is incorrect. This needs to be corrected at the source or a temporary workaround can be added here until then, with this issue being a reminder to fix upstream

bilalshaikh42 commented 2 years ago

Move to biosimulators/biosimulators_utils