"""Annotations for ICG model."""
from sbmlutils.metadata import *
[docs]compartments = {
# liver
"li": [
(BQB.IS, "fma/FMA:7197"),
(BQB.IS, "bto/BTO:0000759"),
(BQB.IS, "ncit/C12392"),
],
"lyso": [
(BQB.IS, "fma/FMA:63836"),
(BQB.IS, "ncit/C13253"),
],
# basolateral membrane
"basolateral": [
(BQB.IS, "fma/FMA:84669"), # Basolateral plasma membrane
(BQB.IS, "go/GO:0016323"), # basolateral plasma membrane
],
# apical membrane
"apical": [
(BQB.IS, "fma/FMA:84666"), # Apical plasma membrane
(BQB.IS, "go/GO:0016324"), # apical plasma membrane
],
"bi": [
(BQB.IS, "fma/FMA:62971"),
(BQB.IS, "ncit/C13192"),
],
# rest
# FIXME: rest compartment is not the organism
"re": [
(BQB.IS_VERSION_OF, "fma/FMA:62955"), # anatomical entity
(BQB.IS_PART_OF, "ncit/C14250"), # Organism
],
# gastrointestinal tract
"gi": [
(BQB.IS, "fma/FMA:71132"),
(BQB.IS, "bto/BTO:0000511"),
(BQB.IS, "ncit/C34082"),
],
# gut/intestine
"gu": [
(BQB.IS, "fma/FMA:45615"), # gut
(BQB.IS, "bto/BTO:0000545"), # gut
(BQB.IS, "ncit/C12736"), # intestine
(BQB.IS, "fma/FMA:7199"), # intestine
(BQB.IS, "bto/BTO:0000648"), # intestine
],
"gu_lumen": [
(BQB.IS, "fma/FMA:14586"), # Lumen of intestine
(BQB.IS, "uberon/UBERON:0018543"), # lumen of intestine
],
# heart
"he": [
(BQB.IS, "ncit/C12727"), # heart
(BQB.IS, "fma/FMA:7088"), # heart
(BQB.IS, "bto/BTO:0000562"), # heart
],
# kidneys
"ki": [
(BQB.IS, "fma/FMA:7203"),
(BQB.IS, "bto/BTO:0000671"),
(BQB.IS, "ncit/C12415"),
],
# lung
"lu": [
(BQB.IS, "fma/FMA:7195"),
(BQB.IS, "bto/BTO:0000763"),
(BQB.IS, "ncit/C12468"),
],
"ve": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
(BQB.IS_PART_OF, "fma/FMA:50723"), # vein
],
"ar": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
(BQB.IS_PART_OF, "fma/FMA:50720"), # artery
],
"po": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
(BQB.IS_PART_OF, "fma/FMA:66645"), # portal vein
],
# hepatic vein
"hv": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
(BQB.IS_PART_OF, "fma/FMA:14337"), # hepatic vein
],
# rest vein
"rev": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
# fixme: be more specific
],
# hepatic vein
"kiv": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
# fixme: be more specific
],
"stomach": [
(BQB.IS, "fma/FMA:7148"),
(BQB.IS, "ncit/C12391"),
(BQB.IS, "uberon/UBERON:0000945"),
(BQB.IS, "bto/BTO:0001307"),
],
# spleen
"sp": [
(BQB.IS, "fma/FMA:7196"),
(BQB.IS, "ncit/C12432"),
(BQB.IS, "uberon/UBERON:0002106"),
(BQB.IS, "bto/BTO:0001281"),
],
# muscle
"mu": [
(BQB.IS, "fma/FMA:30316"),
(BQB.IS, "bto/BTO:0000511"),
(BQB.IS, "ncit/C13056"),
],
"fo": [
(BQB.IS, "ncit/C32628"), # forearm
(BQB.IS, "fma/FMA:9663"), # forearm
],
# hepatic vein
"fov": [
(BQB.IS, "bto/BTO:0000131"), # plasma
(BQB.IS, "ncit/C13356"), # plasma
# fixme: be more specific
],
# pancreas
"pa": [
(BQB.IS, "fma/FMA:7198"),
(BQB.IS, "ncit/C12393"),
(BQB.IS, "uberon/UBERON:0001264"),
(BQB.IS, "bto/BTO:0000988"),
],
"feces": [
(BQB.IS, "fma/FMA:64183"),
(BQB.IS, "ncit/C13234"),
(BQB.IS, "bto/BTO:0000440"),
],
"plasma": [
(BQB.IS, "ncit/C13356"),
(BQB.IS, "bto/BTO:0000131"),
],
"blood": [
(BQB.IS, "fma/FMA:62970"),
(BQB.IS, "ncit/C12434"),
(BQB.IS, "bto/BTO:0000089"),
],
"urine": [
(BQB.IS, "fma/FMA:12274"),
(BQB.IS, "ncit/C13283"),
(BQB.IS, "bto/BTO:0001419"),
],
"parenchyma": [
(BQB.IS, "fma/FMA:45732"),
(BQB.IS, "ncit/C74601"),
(BQB.IS, "bto/BTO:0001539"),
],
"parietal cell": [
(BQB.IS, "ncit/C12594"),
(BQB.IS, "http://snomed.info/id/57041003"),
],
"gastric acid": [
(BQB.IS, "fma/FMA:62972"), # gastric juice
(BQB.IS, "ncit/C94192"),
(BQB.IS, "omit/0006944"), # gastric acid
],
"plasma membrane": [
(BQB.IS, "ncit/C13735"), # Plasma membrane
(BQB.IS, "fma/FMA:63841"), # Plasma membrane
(BQB.IS, "GO:0005886"), # plasma membrane
],
}
[docs]species = {
"bil": [
(BQB.IS, "inchikey/BPYKTIZUTYGOLE-IFADSCNNSA-N"),
(BQB.IS, "chebi/CHEBI:16990"),
(BQB.IS, "ncit/C305"),
],
"icg": [
(BQB.IS, "inchikey/MOFVSTNWEDAEEK-UHFFFAOYSA-M"),
(BQB.IS, "chebi/CHEBI:31696"),
(BQB.IS, "ncit/C65913"),
],
}