Add model annotation details

[stelmo]

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 like Vector{Tuple{String, String, String}}, I think.

See paper: https://www.embopress.org/doi/full/10.15252/msb.20199235

[codecov[bot]]

Codecov Report

Base: 88.44% // Head: 88.77% // Increases project coverage by +0.32% :tada:

Coverage data is based on head (5617d63) compared to base (8484eb3). Patch coverage: 88.88% of modified lines in pull request are covered.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## next #750 +/- ## ========================================== + Coverage 88.44% 88.77% +0.32% ========================================== Files 88 88 Lines 2095 2102 +7 ========================================== + Hits 1853 1866 +13 + Misses 242 236 -6 ``` | [Impacted Files](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | Coverage Δ | | |---|---|---| | [src/types/misc/ObjectModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21pc2MvT2JqZWN0TW9kZWwuamw=) | `66.66% <ø> (ø)` | | | [src/types/models/ObjectModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9PYmplY3RNb2RlbC5qbA==) | `98.85% <80.00%> (-1.15%)` | :arrow_down: | | [src/types/accessors/AbstractMetabolicModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9BYnN0cmFjdE1ldGFib2xpY01vZGVsLmps) | `79.03% <100.00%> (+2.10%)` | :arrow_up: | | [src/types/accessors/ModelWrapper.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9Nb2RlbFdyYXBwZXIuamw=) | `66.66% <100.00%> (+9.52%)` | :arrow_up: | | [src/types/models/JSONModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9KU09OTW9kZWwuamw=) | `98.96% <100.00%> (-0.03%)` | :arrow_down: | | [src/types/misc/gene\_associations.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21pc2MvZ2VuZV9hc3NvY2lhdGlvbnMuamw=) | `91.80% <0.00%> (-3.55%)` | :arrow_down: | | [src/analysis/modifications/knockout.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21vZGlmaWNhdGlvbnMva25vY2tvdXQuamw=) | `100.00% <0.00%> (ø)` | | | [src/reconstruction/enzyme\_constrained.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL2VuenltZV9jb25zdHJhaW5lZC5qbA==) | `100.00% <0.00%> (ø)` | | | [src/types/models/SBMLModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9TQk1MTW9kZWwuamw=) | `93.33% <0.00%> (+1.36%)` | :arrow_up: | | ... and [3 more](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/750?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore)

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[exaexa]

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

[stelmo]

cool, I will add accessors too!

[stelmo]

/format

[stelmo]

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....

[github-actions[bot]]

:heavy_check_mark: Auto-formatting triggered by this comment succeeded, commited as 66bbd8abfe1b28d6b76aa75d201af592255d4b41

[stelmo]

I just added what I could for JSONModel

[stelmo]

/format

[github-actions[bot]]

:heavy_check_mark: Auto-formatting triggered by this comment succeeded, commited as 19266a215fab79b6dae2091e2c44f1c17238b8bd

[stelmo]

It is failing, but this is probably due to an SBML.jl problem