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Update annotations with PBPKO terms
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jwkruisselbrink committed Jul 8, 2024
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78 changes: 40 additions & 38 deletions model/euromix.annotations.csv
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Expand Up @@ -33,44 +33,46 @@ QVen,species,quantity in venous blood,mmol,rdf,BQB_IS,sbo/SBO:0000247,simple che
QExcret,species,quantity excreted in urine (cumulated),mmol,rdf,BQB_IS,sbo/SBO:0000247,simple chemical,
QAir,species,quantity in air,mmol,rdf,BQB_IS,sbo/SBO:0000247,simple chemical,
BM,parameter,body mass,kg,rdf,BQB_IS,http://purl.obolibrary.org/obo/NCIT_C81328,Body mass (or body weight) parameter.,
BM,parameter,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
BSA,parameter,body surface area,dm2,rdf,BQB_IS,http://purl.obolibrary.org/obo/NCIT_C25157,Body surface area (BSA) parameter.,
Height_sc,parameter,thickness stratum corneum,dm,,,,Thickness stratum corneum.,
Height_vs,parameter,thickness viable epidermis,dm,,,,Thickness viable epidermis.,
scVFat,parameter,fat as fraction of total body volume,UNITLESS,,,,,
scVRich,parameter,richly perfused tissues as fraction of total body volume,UNITLESS,,,,,
scVLiver,parameter,liver as fraction of total body volume,UNITLESS,,,,,
scVBlood,parameter,blood as fraction of total body volume,UNITLESS,,,,,
scFBlood,parameter,total blood flow per unit mass,L/(kg.h),,,,,
scFFat,parameter,fat fraction of total blood flow going to compartments,UNITLESS,,,,,
scFPoor,parameter,poorly perfused tissues fraction of total blood flow going to compartments,UNITLESS,,,,,
scFLiver,parameter,liver fraction of total blood flow going to compartments,UNITLESS,,,,,
scFSkin,parameter,skin fraction of total blood flow going to compartments,UNITLESS,,,,,
Falv,parameter,alveolar ventilation rate,L/h,,,,Alveolar ventilation rate.,
rho,parameter,tissue density,kg/L,,,,Density of the tissues.,
PCFat,parameter,partition coefficient fat over blood,UNITLESS,,,,,
PCLiver,parameter,partition coefficient liver over blood,UNITLESS,,,,,
PCRich,parameter,partition coefficient poorly perfused tissue over blood,UNITLESS,,,,,
PCPoor,parameter,partition coefficient richly perfused tissue over blood,UNITLESS,,,,,
PCSkin_sc,parameter,partition coefficient viable skin over stratum corneum,UNITLESS,,,,,
PCSkin,parameter,partition coefficient viable skin over blood,UNITLESS,,,,,
PCAir,parameter,partition coefficient blood over air,UNITLESS,,,,,
Km,parameter,Michaelis constant,mmol,,,,,
BSA,parameter,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
Height_sc,parameter,thickness stratum corneum,dm,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,Thickness stratum corneum.,
Height_vs,parameter,thickness viable epidermis,dm,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,Thickness viable epidermis.,
scVFat,parameter,fat as fraction of total body volume,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scVRich,parameter,richly perfused tissues as fraction of total body volume,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scVLiver,parameter,liver as fraction of total body volume,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scVBlood,parameter,blood as fraction of total body volume,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scFBlood,parameter,total blood flow per unit mass,L/(kg.h),rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scFFat,parameter,fat fraction of total blood flow going to compartments,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scFPoor,parameter,poorly perfused tissues fraction of total blood flow going to compartments,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scFLiver,parameter,liver fraction of total blood flow going to compartments,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
scFSkin,parameter,skin fraction of total blood flow going to compartments,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
Falv,parameter,alveolar ventilation rate,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,Alveolar ventilation rate.,
rho,parameter,tissue density,kg/L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,Density of the tissues.,
PCFat,parameter,partition coefficient fat over blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCLiver,parameter,partition coefficient liver over blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCRich,parameter,partition coefficient poorly perfused tissue over blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCPoor,parameter,partition coefficient richly perfused tissue over blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCSkin_sc,parameter,partition coefficient viable skin over stratum corneum,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCSkin,parameter,partition coefficient viable skin over blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
PCAir,parameter,partition coefficient blood over air,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00167,,
Km,parameter,Michaelis constant,mmol,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00216,Michaelis-Menten constant liver,
Michaelis,parameter,flag for Michaelis-Menten or linear metabolism,UNITLESS,,,,,
Vmax,parameter,maximum rate of metabolism,mmol/(L.h),,,,,
fub,parameter,unbound fraction in blood,UNITLESS,,,,Unbound fraction in blood.,
fSA_exposed,parameter,fraction of skin surface area actually exposed,UNITLESS,,,,,
Kp_sc_vs,parameter,diffusion rate from stratum corneum to viable skin,dm/h,,,,,
kGut,parameter,oral absorption rate constant,/h,,,,Oral 1st order absorption rate constant.,
Vmax,parameter,maximum rate of metabolism,mmol/(L.h),rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00215,Maximum rate of metabolism in liver,
fub,parameter,unbound fraction in blood,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00151,Unbound fraction in blood.,
fSA_exposed,parameter,fraction of skin surface area actually exposed,UNITLESS,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
Kp_sc_vs,parameter,diffusion rate from stratum corneum to viable skin,dm/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
kGut,parameter,oral absorption rate constant,/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,Oral 1st order absorption rate constant.,
CLH,parameter,hepatic clearance rate,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/OMIT_0009720,Hepatic (or metabolic) clearnace rate.,
Ke,parameter,renal excretion rate,L/h,,,,,
f_su,parameter,,L/h,,,,,
f_se,parameter,,L/h,,,,,
VBlood,parameter,total blood volume,L,,,,,
FBlood,parameter,blood flow,L/h,,,,,
FFat,parameter,blood flow to the fat,L/h,,,,,
FPoor,parameter,blood flow to poorly perfused tissues,L/h,,,,,
FLiver,parameter,blood flow to the liver,L/h,,,,,
FSkin,parameter,blood flow to the skin,L/h,,,,,
FRich,parameter,blood flow to richly perfused tissues,L/h,,,,,
FSkin_e,parameter,blood flow to exposed skin,L/h,,,,,
FSkin_u,parameter,blood flow to unexposed skin,L/h,,,,,
Ke,parameter,renal excretion rate,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00240,,
f_su,parameter,,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
f_se,parameter,,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
VBlood,parameter,total blood volume,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FBlood,parameter,blood flow,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FFat,parameter,blood flow to the fat,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FPoor,parameter,blood flow to poorly perfused tissues,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FLiver,parameter,blood flow to the liver,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FSkin,parameter,blood flow to the skin,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FRich,parameter,blood flow to richly perfused tissues,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FSkin_e,parameter,blood flow to exposed skin,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,
FSkin_u,parameter,blood flow to unexposed skin,L/h,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00007,,

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