Notenboom
Notes
DON PBK (Notenboom 2023): GI lumen --kabs--> Liver --Cl_met--> Metabolites Blood <-> Liver, Blood <-> Rest (perfusion-limited)
Overview
| key | value |
|---|---|
| Modelled species/orgamism(s) | http://purl.obolibrary.org/obo/NCBITaxon_9606 |
| Model chemical(s) | http://purl.obolibrary.org/obo/CHEBI_10022 |
| Input route(s) | no routes detected |
| Time resolution | h |
| Amounts unit | mg |
| Volume unit | L |
| Number of compartments | 4 |
| Number of species | 6 |
| Number of parameters | 20 (8 external / 12 internal) |
Diagram
Compartments
| id | name | unit | model qualifier |
|---|---|---|---|
| Lumen | Gut lumen compartment | L | http://purl.obolibrary.org/obo/PBPKO_00478 |
| Liver | Liver compartment | L | http://purl.obolibrary.org/obo/PBPKO_00558 |
| Blood | Blood compartment | L | http://purl.obolibrary.org/obo/PBPKO_00464 |
| Rest | Rest of body compartment | L | http://purl.obolibrary.org/obo/PBPKO_00450 |
Species
| id | name | unit | model qualifier |
|---|---|---|---|
| ALumen | Amount in gut lumen | mg | not specified |
| ALiver | Amount in liver | mg | http://purl.obolibrary.org/obo/PBPKO_00497 |
| ABlood | Amount in blood | mg | http://purl.obolibrary.org/obo/PBPKO_00623 |
| ARest | Amount in rest of body | mg | http://purl.obolibrary.org/obo/PBPKO_00501 |
| ALiverMet1 | Amount of metabolite in liver | mg | http://purl.obolibrary.org/obo/PBPKO_00497 |
| ALiverMet2 | Amount of metabolite in liver | mg | http://purl.obolibrary.org/obo/PBPKO_00497 |
Transfer equations
| id | from | to | equation |
|---|---|---|---|
| _J0 | ALumen | ALiver | kabs * ALumen |
| _J1 | ABlood | ALiver | QL * CBlood |
| _J2 | ALiver | ABlood | QL * CLiver / PL |
| _J3 | ABlood | ARest | QRest * CBlood |
| _J4 | ARest | ABlood | QRest * CRest / PRest |
| _J5 | ALiver | ALiverMet1 | CLintMet1 * CLiver |
| _J6 | ALiver | ALiverMet2 | CLintMet2 * CLiver |
ODEs
\(\frac{d[\mathtt{ALumen}]}{dt} = - \mathit{kabs}\cdot \mathit{ALumen}\)
\(\frac{d[\mathtt{ALiver}]}{dt} = \mathit{kabs}\cdot \mathit{ALumen} + \mathit{QL}\cdot \mathit{CBlood} - \frac{\mathit{QL}\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{CLintMet1}\cdot \mathit{CLiver} - \mathit{CLintMet2}\cdot \mathit{CLiver}\)
\(\frac{d[\mathtt{ABlood}]}{dt} = - \mathit{QL}\cdot \mathit{CBlood} + \frac{\mathit{QL}\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{QRest}\cdot \mathit{CBlood} + \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{ARest}]}{dt} = \mathit{QRest}\cdot \mathit{CBlood} - \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{ALiverMet1}]}{dt} = \mathit{CLintMet1}\cdot \mathit{CLiver}\)
\(\frac{d[\mathtt{ALiverMet2}]}{dt} = \mathit{CLintMet2}\cdot \mathit{CLiver}\)
Assignment rules
| variable | assignment |
|---|---|
| VL | VLc * BW |
| VB | VBc * BW |
| VRest | 0.84 * BW - VL - VB |
| QC | 15 * pow(BW, 0.74) |
| QL | QLc * QC |
| QRest | (1 - QLc) * QC |
| CLintMet1 | 0.07 * BW |
| CLintMet2 | 0.32 * BW |
| CLumen | ALumen / Lumen |
| CLiver | ALiver / Liver |
| CBlood | ABlood / Blood |
| CRest | ARest / Rest |
Initial assignments
| variable | assignment |
|---|---|
| Lumen | VLum |
| Liver | VL |
| Blood | VB |
| Rest | VRest |
Parameters
| id | name | unit | model qualifier |
|---|---|---|---|
| BW | Bodyweight | kg | http://purl.obolibrary.org/obo/PBPKO_00008 |
| VLc | Volume fraction of liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00078 |
| VBc | Volume fraction of blood | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00104 |
| VL | Volume of liver | L | http://purl.obolibrary.org/obo/PBPKO_00077 |
| VB | Volume of blood | L | http://purl.obolibrary.org/obo/PBPKO_00108 |
| VLum | Volume of gut lumen | L | not specified |
| VRest | Volume of rest of body | L | http://purl.obolibrary.org/obo/PBPKO_00105 |
| QC | Cardiac output | L/h | http://purl.obolibrary.org/obo/PBPKO_00013 |
| QLc | Cardiac output fraction to liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00025 |
| QL | Cardiac output to liver | L/h | http://purl.obolibrary.org/obo/PBPKO_00024 |
| QRest | Cardiac output to rest of body | L/h | http://purl.obolibrary.org/obo/PBPKO_00050 |
| kabs | Absorption constant from GI to liver | /h | http://purl.obolibrary.org/obo/PBPKO_00141 |
| CLintMet1 | Metabolic clearance rate | L/h | http://purl.obolibrary.org/obo/PBPKO_00234 |
| CLintMet2 | Metabolic clearance rate | L/h | http://purl.obolibrary.org/obo/PBPKO_00234 |
| PL | Partition coefficient blood-liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00577 |
| PRest | Partition coefficient blood- rest body | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00585 |
| CLumen | Concentration in lumen | mg/L | not specified |
| CLiver | Concentration in liver | mg/L | http://purl.obolibrary.org/obo/PBPKO_00539 |
| CBlood | Concentration in blood | mg/L | http://purl.obolibrary.org/obo/PBPKO_00301 |
| CRest | Concentration in rest of body | mg/L | http://purl.obolibrary.org/obo/PBPKO_00548 |