Metabolic model IDs #2072
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Metabolic model IDs #2072
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… `proteinorthology` module
…nce db in `reference_ids` attribute
…nce db in `reference_ids` attribute
…` object from an `AnvioKOAnnotation`
…erence source in the ModelSEED Biochemistry database
…e KBase ID as the first ID and then IDs from other references in the `reference_ids` attribute
…e KBase ID as the first ID and then IDs from other references in the `reference_ids` attribute
…tion `notes` rather than `annotations`
…ns, following format of E. coli core model
…cellular compartment
…s rather than annotation section
…annotations, following format of E. coli core model
…me manner as pangenome
…olic-model-ids
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This PR updates the anvi'o
proteinorthologysubpackage, which tracks reactions and metabolites associated with proteins and contains the backend ofanvi-get-metabolic-model-file, which generates a COBRApy JSON file representing the metabolic network of a genome or pangenome. The script currently relies upon KEGG KOfam annotations and the ModelSEED Biochemistry database for reaction information. The PR changes how IDs are assigned to reaction and metabolite objects in the JSON file, with the ID now always being the KBase ID from ModelSEED, and alternate IDs, such as KEGG Reaction and Compound IDs and BiGG IDs cross-referenced in ModelSEED, supplemented as object annotations. Other changes in the PR ensued from this, including the structure of classes inproteinorthology.protein, includingChemicalandAnvioKOAnnotation.