feat: provide the stoichiometric matrix with comprehensive external association and annotation

[haowang-bioinfo]

Description of the issue:

• GEMs are mathematical representations of biochemistry and molecular biology. The GEM reconstruction and curation can be viewed as an iterative process of incorporating biological information from databases and literature.
• HumanGEM aims to provide comprehensive coverage of human metabolism, which is reflected through continuous curation of stoichiometric matrix.
• To increase scalability and robustness for the model, it is thus expected to comprehensively associate reactions and metabolites to external identifiers in major databases and GEMs.

Expected feature/value/output:

• Specify the JSON format for storing the association/annotation information (#75)
• Define a list of external database (e.g. MetaNetX, KEGG, MetaCyc) whose identifiers need to be provided
• Develop functions/scripts allowing regular curation of exteranl association/annotation, and consistency checks among inter-associated identifiers

I hereby confirm that I have:

• [X] Checked that a similar issue does not exist already

[haowang-bioinfo]

The Human1 reactions are annotated with external identifiers from 4 major databases (KEGG, BiGG, REACTOME, MetaNetX) and 3 previous Human GEMs (EHMN, HepatoNET1 and Recon3D). This annotation/association has been provided in humanGEMRxnAssoc.JSON.

[haowang-bioinfo]

The Human1 metabolites are annotated with external identifiers from 7 major databases (KEGG, BiGG, HMDB, ChEBI, PubChem, LipidMaps, MetaNetX) and 3 previous Human GEMs (EHMN, HepatoNET1 and Recon3D). This annotation/association has been provided in humanGEMMetAssoc.JSON.

[haowang-bioinfo]

Now the stoichiometric matrix annotation collected from various external sources has been centralized into 2 JSON files, which should be synced with the model structure (i.e. rxns and mets fields) whenever HumanGEM stoichiometric matrix is modified.