# -*- coding: utf-8 -*-
"""Lists and annotations for compartment names and reactions.
Please send a PR if you want to add something here :)
"""
[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 list of sub-strings in reaction IDs that usually indicate
that the reaction is *not* a reaction of the specified type."""
[docs]sbo_terms = {"demand": "SBO:0000628",
"exchange": "SBO:0000627",
"sink": "SBO:0000632",
"biomass": "SBO:0000629",
"pseudoreaction": "SBO:0000631"}
"""SBO term identifiers for various boundary types."""
[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"]
}
"""A list of common compartment abbreviations and alternative names."""