annotations¶
The annotations of the recurring compartments of the models.
An annotation is a list of (qualifier, resource) pairs: the qualifier is a
biological qualifier of sbmlutils.metadata.BQB and the resource a term of an
ontology, written as collection/term of identifiers.org. sbmlutils writes
them as the RDF of the element they are given to, e.g.
Compartment("Vli", ..., annotations=compartments["li"]) for the liver.
module-attribute
¶
compartments = {
"fluid volume": [],
"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": [
(BQB.IS, "fma/FMA:84669"),
(BQB.IS, "go/GO:0016323"),
],
"apical": [
(BQB.IS, "fma/FMA:84666"),
(BQB.IS, "go/GO:0016324"),
],
"bi": [
(BQB.IS, "fma/FMA:62971"),
(BQB.IS, "ncit/C13192"),
],
"re": [
(BQB.IS_VERSION_OF, "fma/FMA:62955"),
(BQB.IS_PART_OF, "ncit/C14250"),
],
"gi": [
(BQB.IS, "fma/FMA:71132"),
(BQB.IS, "bto/BTO:0000511"),
(BQB.IS, "ncit/C34082"),
],
"gu": [
(BQB.IS, "bto/BTO:0000545"),
(BQB.IS, "ncit/C12736"),
(BQB.IS, "fma/FMA:7199"),
(BQB.IS, "bto/BTO:0000648"),
],
"gu_lumen": [
(BQB.IS, "fma/FMA:14586"),
(BQB.IS, "uberon/UBERON:0018543"),
],
"duodenum": [
(BQB.IS, "fma/FMA:7206"),
(BQB.IS, "uberon/UBERON:0002114"),
],
"jejunum": [
(BQB.IS, "fma/FMA:7207"),
(BQB.IS, "uberon/UBERON:0002115"),
],
"ileum": [
(BQB.IS, "fma/FMA:7208"),
(BQB.IS, "uberon/UBERON:0002116"),
],
"colon": [
(BQB.IS, "fma/FMA:14543"),
(BQB.IS, "uberon/UBERON:0001155"),
],
"he": [
(BQB.IS, "ncit/C12727"),
(BQB.IS, "fma/FMA:7088"),
(BQB.IS, "bto/BTO:0000562"),
],
"ki": [
(BQB.IS, "fma/FMA:7203"),
(BQB.IS, "bto/BTO:0000671"),
(BQB.IS, "ncit/C12415"),
],
"lu": [
(BQB.IS, "fma/FMA:7195"),
(BQB.IS, "bto/BTO:0000763"),
(BQB.IS, "ncit/C12468"),
],
"ve": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "fma/FMA:50723"),
],
"ar": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "fma/FMA:50720"),
],
"po": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "fma/FMA:66645"),
],
"hv": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "fma/FMA:14337"),
],
"rv": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "bto/BTO:0002681"),
(BQB.IS_PART_OF, "ncit/C33462"),
(BQB.IS_PART_OF, "fma/FMA:14334"),
],
"rev": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
],
"kiv": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
],
"stomach": [
(BQB.IS, "fma/FMA:7148"),
(BQB.IS, "ncit/C12391"),
(BQB.IS, "uberon/UBERON:0000945"),
(BQB.IS, "bto/BTO:0001307"),
],
"sp": [
(BQB.IS, "fma/FMA:7196"),
(BQB.IS, "ncit/C12432"),
(BQB.IS, "uberon/UBERON:0002106"),
(BQB.IS, "bto/BTO:0001281"),
],
"mu": [
(BQB.IS, "fma/FMA:30316"),
(BQB.IS, "bto/BTO:0000887"),
(BQB.IS, "ncit/C13056"),
],
"fo": [
(BQB.IS, "ncit/C32628"),
(BQB.IS, "fma/FMA:9663"),
],
"fov": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
],
"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:9670"),
(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, "snomedct/57041003"),
],
"gastric acid": [
(BQB.IS, "fma/FMA:62972"),
(BQB.IS, "ncit/C94192"),
(BQB.IS, "omit/0006944"),
],
"plasma membrane": [
(BQB.IS, "ncit/C13735"),
(BQB.IS, "fma/FMA:63841"),
(BQB.IS, "go/GO:0005886"),
],
}
The annotations of the compartments, keyed by their abbreviation in the models.
li liver, ki kidney, gu gut, ve and ar the venous and the arterial
blood, po the portal vein, urine, feces, ...