Closed stelmo closed 1 year ago
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PS it would be useful to probably make accessors for that, model_annotations and model_notes is OK. Not sure if that encodes to JSON but SBML should be very much OK
cool, I will add accessors too!
/format
So unfortunately JSON model is not really standardized, I am not sure where they would store this kind of information. They do have an id
field at the top level of the object, but that is about it....
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I just added what I could for JSONModel
/format
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It is failing, but this is probably due to an SBML.jl problem
Since ObjectModel is the go-to model type, it should contain as much info as possible. The latest community standards paper actually lists some of the requirements that models should possess. Much of this information can be included already into the annotations fields for Reactions, Metabolites and Genes. However, the model lacks these fields. Here I just co-opt these for the model. The only drawback is that
Annotations
is just a dictionary, and to be miriam compliant it should be a vector of tuples likeVector{Tuple{String, String, String}}
, I think.See paper: https://www.embopress.org/doi/full/10.15252/msb.20199235