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.
The PBPK library (pkpdsim.pbpk.annotation) takes the terms of its organs,
blood pools, lumen and tubule segments and sampling sites from here and adds
the terms of the PBPK ontology.
module-attribute
¶
compartments = {
"fluid volume": [
(BQB.IS, "mesh/D045604"),
(BQB.IS_VERSION_OF, "ncit/C13236"),
],
"li": [
(BQB.IS, "fma/FMA:7197"),
(BQB.IS, "bto/BTO:0000759"),
(BQB.IS, "ncit/C12392"),
(BQB.IS, "uberon/UBERON:0002107"),
],
"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"),
(BQB.IS_PART_OF, "uberon/UBERON:0000468"),
],
"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"),
(BQB.IS, "uberon/UBERON:0000948"),
],
"ki": [
(BQB.IS, "fma/FMA:7203"),
(BQB.IS, "bto/BTO:0000671"),
(BQB.IS, "ncit/C12415"),
(BQB.IS, "uberon/UBERON:0002113"),
],
"lu": [
(BQB.IS, "fma/FMA:7195"),
(BQB.IS, "bto/BTO:0000763"),
(BQB.IS, "ncit/C12468"),
(BQB.IS, "uberon/UBERON:0002048"),
],
"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"),
(BQB.IS_PART_OF, "uberon/UBERON:0004582"),
(BQB.IS_PART_OF, "ncit/C12814"),
],
"kiv": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "uberon/UBERON:0001140"),
(BQB.IS_PART_OF, "ncit/C33462"),
],
"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"),
(BQB.IS, "uberon/UBERON:0001134"),
],
"fo": [
(BQB.IS, "ncit/C32628"),
(BQB.IS, "fma/FMA:9663"),
],
"fov": [
(BQB.IS, "bto/BTO:0000131"),
(BQB.IS, "ncit/C13356"),
(BQB.IS_PART_OF, "ncit/C12814"),
(BQB.IS_PART_OF, "ncit/C32628"),
],
"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"),
(BQB.IS, "uberon/UBERON:0001969"),
],
"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"),
],
"br": [
(BQB.IS, "uberon/UBERON:0000955"),
(BQB.IS, "ncit/C12439"),
],
"si": [
(BQB.IS, "uberon/UBERON:0002108"),
(BQB.IS, "ncit/C12386"),
],
"la": [
(BQB.IS, "uberon/UBERON:0000059"),
(BQB.IS, "ncit/C12379"),
],
"sk": [
(BQB.IS, "uberon/UBERON:0002097"),
(BQB.IS, "ncit/C12470"),
],
"ad": [
(BQB.IS, "uberon/UBERON:0001013"),
(BQB.IS, "ncit/C12472"),
],
"bo": [
(BQB.IS, "uberon/UBERON:0002481"),
(BQB.IS, "ncit/C12366"),
],
"go": [
(BQB.IS, "uberon/UBERON:0000991"),
(BQB.IS, "ncit/C12725"),
],
"caecum": [
(BQB.IS, "uberon/UBERON:0001153"),
(BQB.IS, "ncit/C12381"),
],
"ascending colon": [
(BQB.IS, "uberon/UBERON:0001156"),
(BQB.IS, "ncit/C12265"),
],
"transverse colon": [
(BQB.IS, "uberon/UBERON:0001157"),
(BQB.IS, "ncit/C12385"),
],
"descending colon": [
(BQB.IS, "uberon/UBERON:0001158"),
(BQB.IS, "ncit/C12268"),
],
"sigmoid colon": [
(BQB.IS, "uberon/UBERON:0001159"),
(BQB.IS, "ncit/C12384"),
],
"rectum": [
(BQB.IS, "uberon/UBERON:0001052"),
(BQB.IS, "ncit/C12390"),
],
"proximal tubule": [(BQB.IS, "uberon/UBERON:0004134")],
"loop of Henle": [(BQB.IS, "uberon/UBERON:0001288")],
"distal tubule": [(BQB.IS, "uberon/UBERON:0004135")],
"collecting duct": [(BQB.IS, "uberon/UBERON:0001232")],
"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, ...