Wang
Notes
DON PBK (Wang et al., human, compact): Stomach → Jejunum → Ileum → LI; absorption from each segment → Intestinal tissue → liver Liver perfusion-limited (venous) + intrinsic clearance; Blood ↔ Rest
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 | umol |
| Volume unit | L |
| Number of compartments | 8 |
| Number of species | 9 |
| Number of parameters | 48 (15 external / 33 internal) |
Diagram
Compartments
| id | name | unit | model qualifier |
|---|---|---|---|
| Stomach | Stomach compartment | L | http://purl.obolibrary.org/obo/PBPKO_00566 |
| Jejunum | Jejunum compartment | L | http://purl.obolibrary.org/obo/PBPKO_00482 |
| Ileum | Ileum compartment | L | http://purl.obolibrary.org/obo/PBPKO_00481 |
| LargeLumen | Large intestine lumen compartment | L | http://purl.obolibrary.org/obo/PBPKO_00474 |
| 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 |
| IntestinalTissue | Intestinal tissue compartment | L | not specified |
Species
| id | name | unit | model qualifier |
|---|---|---|---|
| ASt | Amount in stomach | umol | not specified |
| AJ | Amount in jejunum | umol | not specified |
| AI | Amount in ileum | umol | not specified |
| ALI | amount in large intestine | umol | not specified |
| AIT | Amount in intestinal tissue | umol | not specified |
| ALiver | Amount in liver | umol | http://purl.obolibrary.org/obo/PBPKO_00497 |
| ABlood | Amount in blood | umol | http://purl.obolibrary.org/obo/PBPKO_00623 |
| ARest | Amount in rest of body | umol | http://purl.obolibrary.org/obo/PBPKO_00501 |
| AMet | Amount metabolised | umol | http://purl.obolibrary.org/obo/PBPKO_00497 |
Transfer equations
| id | from | to | equation |
|---|---|---|---|
| _J0 | ASt | AJ | ksto * ASt |
| _J1 | AJ | AI | kt1 * AJ |
| _J2 | AI | ALI | kt2 * AI |
| _J3 | AJ | AIT | kabsJ * CJ |
| _J4 | AI | AIT | kabsI * CI |
| _J5 | ALI | AIT | kabsLI * CLI |
| _J6 | ABlood | AIT | QIT * CBlood |
| _J7 | AIT | ALiver | QIT * CIT / PIT |
| _J8 | ABlood | ALiver | QL * CBlood |
| _J9 | ALiver | ABlood | (QL + QIT) * CLiver / PL |
| _J10 | ABlood | ARest | QRest * CBlood |
| _J11 | ARest | ABlood | QRest * CRest / PRest |
| _J12 | ALiver | AMet | CLint * (CLiver / PL) |
ODEs
\(\frac{d[\mathtt{ASt}]}{dt} = - \mathit{ksto}\cdot \mathit{ASt}\)
\(\frac{d[\mathtt{AJ}]}{dt} = \mathit{ksto}\cdot \mathit{ASt} - \mathit{kt1}\cdot \mathit{AJ} - \mathit{kabsJ}\cdot \mathit{CJ}\)
\(\frac{d[\mathtt{AI}]}{dt} = \mathit{kt1}\cdot \mathit{AJ} - \mathit{kt2}\cdot \mathit{AI} - \mathit{kabsI}\cdot \mathit{CI}\)
\(\frac{d[\mathtt{ALI}]}{dt} = \mathit{kt2}\cdot \mathit{AI} - \mathit{kabsLI}\cdot \mathit{CLI}\)
\(\frac{d[\mathtt{AIT}]}{dt} = \mathit{kabsJ}\cdot \mathit{CJ} + \mathit{kabsI}\cdot \mathit{CI} + \mathit{kabsLI}\cdot \mathit{CLI} + \mathit{QIT}\cdot \mathit{CBlood} - \frac{\mathit{QIT}\cdot \mathit{CIT}}{\mathit{PIT}}\)
\(\frac{d[\mathtt{ALiver}]}{dt} = \frac{\mathit{QIT}\cdot \mathit{CIT}}{\mathit{PIT}} + \mathit{QL}\cdot \mathit{CBlood} - \frac{(\mathit{QL}+\mathit{QIT})\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{CLint}\cdot \frac{\mathit{CLiver}}{\mathit{PL}}\)
\(\frac{d[\mathtt{ABlood}]}{dt} = - \mathit{QIT}\cdot \mathit{CBlood} - \mathit{QL}\cdot \mathit{CBlood} + \frac{(\mathit{QL}+\mathit{QIT})\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{QRest}\cdot \mathit{CBlood} + \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{ARest}]}{dt} = \mathit{QRest}\cdot \mathit{CBlood} - \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{AMet}]}{dt} = \mathit{CLint}\cdot \frac{\mathit{CLiver}}{\mathit{PL}}\)
Assignment rules
| variable | assignment |
|---|---|
| VL | VLc * BW |
| VB | VBc * BW |
| VIT | VITc * BW |
| VJ | 3.14159 * pow(Ddm / 2, 2) * LJdm |
| VI | 3.14159 * pow(Ddm / 2, 2) * LIdm |
| VLI | 0.561 |
| SAJ | 3.14159 * Ddm * LJdm |
| SAI | 3.14159 * Ddm * LIdm |
| SALI | 3.14159 * Ddm * LLIdm |
| VRest | 0.84 * BW - VL - VB - VIT |
| QC | 15 * pow(BW, 0.74) |
| QLc | 0.046 |
| QITc | 0.181 |
| QL | QLc * QC |
| QIT | QITc * QC |
| QRest | QC - QL - QIT |
| PL | 0.76 / RBP |
| PIT | 0.73 / RBP |
| PRest | 1 / RBP |
| Papp_dm_h | PappDONc / 10000 * (3600/10) |
| kabsJ | Papp_dm_h * SAJ |
| kabsI | Papp_dm_h * SAI |
| kabsLI | Papp_dm_h * SALI |
| CLint | 0.008 * 32 * VLc * 1000 * BW * 60 / 1000 |
| CSt | ASt / Stomach |
| CJ | AJ / Jejunum |
| CI | AI / Ileum |
| CLI | ALI / LargeLumen |
| CIT | AIT / IntestinalTissue |
| CLiver | ALiver / Liver |
| CBlood | ABlood / Blood |
| CRest | ARest / Rest |
| Met | CLint * (CLiver / PL) |
Initial assignments
| variable | assignment |
|---|---|
| Jejunum | VJ |
| Ileum | VI |
| LargeLumen | VLI |
| 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 | not specified |
| VITc | Volume fraction of intestinal tissue | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00070 |
| VL | Volume of liver | L | http://purl.obolibrary.org/obo/PBPKO_00077 |
| VB | Volume of blood | L | http://purl.obolibrary.org/obo/PBPKO_00108 |
| VIT | Volume of Intestinal tissue | L | http://purl.obolibrary.org/obo/PBPKO_00069 |
| Ddm | Intestinal segment geometry - diameter | dm | not specified |
| LJdm | Intestinal segment geometry - jejunum length | dm | not specified |
| LIdm | Intestinal segment geometry - ileum length | dm | not specified |
| LLIdm | Intestinal segment geometry - large intestine length | dm | not specified |
| VJ | Volume of jejunum | L | http://purl.obolibrary.org/obo/PBPKO_00425 |
| VI | Volume of ileum | L | http://purl.obolibrary.org/obo/PBPKO_00426 |
| VLI | Volume of large intestine lumen | L | http://purl.obolibrary.org/obo/PBPKO_00073 |
| SAJ | Surface area - jejunum lumen | dm^2 | http://purl.obolibrary.org/obo/PBPKO_00010 |
| SAI | Surface area - ileum lumen | dm^2 | http://purl.obolibrary.org/obo/PBPKO_00010 |
| SALI | Surface area - large intestine lumen | dm^2 | http://purl.obolibrary.org/obo/PBPKO_00010 |
| 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 |
| QITc | Cardiac output fraction to intestinal tissue | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00017 |
| QL | Cardiac output to liver | L/h | http://purl.obolibrary.org/obo/PBPKO_00024 |
| QIT | Cardiac output to intestinal tissue | L/h | http://purl.obolibrary.org/obo/PBPKO_00016 |
| QRest | Cardiac output to rest of body | L/h | http://purl.obolibrary.org/obo/PBPKO_00050 |
| RBP | Blood to plasma ratio | dimensionless | not specified |
| fu | Fraction unbound | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00591 |
| PL | Partition coefficient blood-liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00577 |
| PIT | Partition coefficient intestinal tissue - blood | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00574 |
| PRest | Partition coefficient blood- rest body | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00585 |
| ksto | Kinetic constant stomach to jejunum | /h | not specified |
| kt1 | Kinetic constant jejunum to ileum | /h | not specified |
| kt2 | Kinetic constant ileum to large intestine | /h | not specified |
| PappDONc | Intestinal absorption rate | not specified | http://purl.obolibrary.org/obo/PBPKO_00142 |
| Papp_dm_h | Intestinal absorption rate | dm/h | http://purl.obolibrary.org/obo/PBPKO_00142 |
| kabsJ | Absorption rate jejunum | L/h | not specified |
| kabsI | Absorption rate ileum | L/h | not specified |
| kabsLI | Absorption rate large intestine | L/h | not specified |
| CLint | Hepatic intrinsic clearance | L/h | http://purl.obolibrary.org/obo/PBPKO_00235 |
| ALiv | Amount in liver | umol | http://purl.obolibrary.org/obo/PBPKO_00497 |
| CSt | Concentration in stomach | umol/L | not specified |
| CJ | Concentration in jejunum | umol/L | not specified |
| CI | Concentration in ileum | umol/L | not specified |
| CLI | Concentration in large intestine | umol/L | not specified |
| CIT | Concentration in intestinal tissue | umol/L | not specified |
| CLiver | Concentration in liver | umol/L | http://purl.obolibrary.org/obo/PBPKO_00539 |
| CBlood | Concentration in blood | umol/L | http://purl.obolibrary.org/obo/PBPKO_00301 |
| CRest | Concentration in rest of body | umol/L | http://purl.obolibrary.org/obo/PBPKO_00548 |
| Met | Hepatic metabolism | umol/L | http://purl.obolibrary.org/obo/PBPKO_00234 |