Source code for cobra.medium.annotations

"""Provide lists and annotations for compartment names and reactions.

Please send a PR if you want to add something here :)


# A dictionary having keys as reaction types and keys as prefixes of
# reaction IDs that usually indicate that the reaction is *not* a reaction
# of the specified type.
[docs]excludes = { "demand": ["SN_", "SK_", "sink", "EX_", "exchange"], "exchange": [ "demand", "DM_", "biosynthesis", "transcription", "replication", "SN_", "SK_", "sink", ], "sink": [ "demand", "DM_", "biosynthesis", "transcription", "replication", "EX_", "exchange",
], } # A dictionary having SBO term identifiers as values and boundary types # as keys.
[docs]sbo_terms = { "demand": "SBO:0000628", "exchange": "SBO:0000627", "sink": "SBO:0000632", "biomass": "SBO:0000629", "pseudoreaction": "SBO:0000631",
} # A dictionary having keys as common compartment abbreviations and values # as alternative names.
[docs]compartment_shortlist = { "ce": ["cell envelope"], "c": [ "cytoplasm", "cytosol", "default", "in", "intra cellular", "intracellular", "intracellular region", "intracellular space", ], "er": ["endoplasmic reticulum"], "erm": ["endoplasmic reticulum membrane"], "e": [ "extracellular", "extraorganism", "out", "extracellular space", "extra organism", "extra cellular", "extra-organism", "external", "external medium", ], "f": ["flagellum", "bacterial-type flagellum"], "g": ["golgi", "golgi apparatus"], "gm": ["golgi membrane"], "h": ["chloroplast"], "l": ["lysosome"], "im": ["mitochondrial intermembrane space"], "mm": ["mitochondrial membrane"], "m": ["mitochondrion", "mitochondria"], "n": ["nucleus"], "p": ["periplasm", "periplasmic space"], "x": ["peroxisome", "glyoxysome"], "u": ["thylakoid"], "vm": ["vacuolar membrane"], "v": ["vacuole"], "w": ["cell wall"], "s": ["eyespot", "eyespot apparatus", "stigma"],