Shin
Notes
BPA PBK - Shin et al. 2004 SILume -> SITissue -> Liver <- Spleen, Stomach via portal vein Perfusion-limited: Blood <-> Liver, Blood <-> Rest Hepatic metabolism: intrinsic clearance
Overview
| key | value |
|---|---|
| Modelled species/orgamism(s) | http://purl.obolibrary.org/obo/NCBITaxon_9606 |
| Model chemical(s) | http://purl.obolibrary.org/obo/CHEBI_33216 |
| Input route(s) | no routes detected |
| Time resolution | h |
| Amounts unit | mg |
| Volume unit | L |
| Number of compartments | 7 |
| Number of species | 8 |
| Number of parameters | 29 (8 external / 21 internal) |
Diagram
Compartments
| id | name | unit | model qualifier |
|---|---|---|---|
| Stomach | stomach | L | http://purl.obolibrary.org/obo/PBPKO_00566 |
| IntestinalLumen | GI lumen compartment | L | http://purl.obolibrary.org/obo/PBPKO_00478 |
| Spleen | spleen | L | http://purl.obolibrary.org/obo/PBPKO_00492 |
| SmallIntestine | Small intestine compartment | L | http://purl.obolibrary.org/obo/PBPKO_00472 |
| Liver | liver | L | http://purl.obolibrary.org/obo/PBPKO_00558 |
| Blood | blood | L | http://purl.obolibrary.org/obo/PBPKO_00464 |
| Rest | rest-of-body | L | http://purl.obolibrary.org/obo/PBPKO_00450 |
Species
| id | name | unit | model qualifier |
|---|---|---|---|
| ASt | Amount in stomach | mg | not specified |
| AIL | Amount in GI lumen | mg | http://purl.obolibrary.org/obo/PBPKO_00496 |
| ASpleen | Amount in spleen | mg | not specified |
| ASI | Amount in small intestine | mg | not specified |
| ALiver | amount of chemical in liver | mg | http://purl.obolibrary.org/obo/PBPKO_00497 |
| ABlood | amount of chemical in blood | mg | http://purl.obolibrary.org/obo/PBPKO_00623 |
| ARest | amount of chemical in rest-of-body | mg | http://purl.obolibrary.org/obo/PBPKO_00501 |
| AMet | Amount in liver | mg | http://purl.obolibrary.org/obo/PBPKO_00497 |
Transfer equations
| id | from | to | equation |
|---|---|---|---|
| _J0 | AIL | ASI | kabs * AIL |
| _J1 | ASI | ALiver | QSI * CSI / PSI |
| _J2 | ABlood | ASI | QSI * CBlood |
| _J3 | ASpleen | ALiver | QSpleen * CSpleen / PSpleen |
| _J4 | ABlood | ASpleen | QSpleen * CBlood |
| _J5 | ASt | ALiver | QSt * CSt / PSt |
| _J6 | ABlood | ASt | QSt * CBlood |
| _J7 | ABlood | ALiver | (QL - QSpleen - QSt - QSI) * CBlood |
| _J8 | ALiver | ABlood | QL * CLiver / PL |
| _J9 | ABlood | ARest | QRest * CBlood |
| _J10 | ARest | ABlood | QRest * CRest / PRest |
| _J11 | ALiver | AMet | CLint * (CLiver / PL) |
ODEs
\(\frac{d[\mathtt{ASt}]}{dt} = - \frac{\mathit{QSt}\cdot \mathit{CSt}}{\mathit{PSt}} + \mathit{QSt}\cdot \mathit{CBlood}\)
\(\frac{d[\mathtt{AIL}]}{dt} = - \mathit{kabs}\cdot \mathit{AIL}\)
\(\frac{d[\mathtt{ASpleen}]}{dt} = - \frac{\mathit{QSpleen}\cdot \mathit{CSpleen}}{\mathit{PSpleen}} + \mathit{QSpleen}\cdot \mathit{CBlood}\)
\(\frac{d[\mathtt{ASI}]}{dt} = \mathit{kabs}\cdot \mathit{AIL} - \frac{\mathit{QSI}\cdot \mathit{CSI}}{\mathit{PSI}} + \mathit{QSI}\cdot \mathit{CBlood}\)
\(\frac{d[\mathtt{ALiver}]}{dt} = \frac{\mathit{QSI}\cdot \mathit{CSI}}{\mathit{PSI}} + \frac{\mathit{QSpleen}\cdot \mathit{CSpleen}}{\mathit{PSpleen}} + \frac{\mathit{QSt}\cdot \mathit{CSt}}{\mathit{PSt}} + (\mathit{QL}-\mathit{QSpleen}-\mathit{QSt}-\mathit{QSI})\cdot \mathit{CBlood} - \frac{\mathit{QL}\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{CLint}\cdot \frac{\mathit{CLiver}}{\mathit{PL}}\)
\(\frac{d[\mathtt{ABlood}]}{dt} = - \mathit{QSI}\cdot \mathit{CBlood} - \mathit{QSpleen}\cdot \mathit{CBlood} - \mathit{QSt}\cdot \mathit{CBlood} - (\mathit{QL}-\mathit{QSpleen}-\mathit{QSt}-\mathit{QSI})\cdot \mathit{CBlood} + \frac{\mathit{QL}\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{QRest}\cdot \mathit{CBlood} + \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{ARest}]}{dt} = \mathit{QRest}\cdot \mathit{CBlood} - \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{AMet}]}{dt} = \mathit{CLint}\cdot \frac{\mathit{CLiver}}{\mathit{PL}}\)
Assignment rules
| variable | assignment |
|---|---|
| VL | 1700 / 1000 |
| VB | 5530 / 1000 |
| VSt | 200 / 1000 |
| VSpleen | 200 / 1000 |
| VSI | 1700 / 1000 |
| VRest | 0.84 * BW - VL - VB - VSt - VSI - VSpleen |
| QC | 15 * pow(BW, 0.74) |
| QL | 1646.7 / (1000 * 60) |
| QSpleen | 76.7 / (1000 * 60) |
| QSt | 38.3 / (1000 * 60) |
| QSI | 1100 / (1000 * 60) |
| QRest | QC - QL - QSpleen - QSt - QSI |
| kabs | 0.0006 * 60 |
| CIL | AIL / IntestinalLumen |
| CSI | ASI / SmallIntestine |
| CSpleen | ASpleen / Spleen |
| CSt | ASt / Stomach |
| CLiver | ALiver / Liver |
| CBlood | ABlood / (Blood * RBS) |
| CRest | ARest / Rest |
| Met | CLint * (CLiver / PL) |
Initial assignments
| variable | assignment |
|---|---|
| Stomach | VSt |
| Spleen | VSpleen |
| SmallIntestine | VSI |
| Liver | VL |
| Blood | VB |
| Rest | VRest |
Parameters
| id | name | unit | model qualifier |
|---|---|---|---|
| BW | body weight | kg | http://purl.obolibrary.org/obo/PBPKO_00008 |
| VL | Volume of liver | L | http://purl.obolibrary.org/obo/PBPKO_00077 |
| VB | Volume of blood | L | http://purl.obolibrary.org/obo/PBPKO_00108 |
| VSt | Volume of stomach | L | http://purl.obolibrary.org/obo/PBPKO_00067 |
| VSpleen | Volume of spleen | L | http://purl.obolibrary.org/obo/PBPKO_00095 |
| VSI | Volume of small intestine | L | http://purl.obolibrary.org/obo/PBPKO_00071 |
| 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 |
| QL | Blood flow to liver | L/h | http://purl.obolibrary.org/obo/PBPKO_00024 |
| QSpleen | Blood flow to spleen | L/h | http://purl.obolibrary.org/obo/PBPKO_00042 |
| QSt | Blood flow to stomach | L/h | http://purl.obolibrary.org/obo/PBPKO_00014 |
| QSI | Blood flow to small intestine | L/h | http://purl.obolibrary.org/obo/PBPKO_00018 |
| QRest | Blood flow to rest of body | L/h | http://purl.obolibrary.org/obo/PBPKO_00050 |
| RBS | Blood serum ratio | dimensionless | not specified |
| PL | Partition coefficient - liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00577 |
| PSpleen | Partition coefficient - spleen | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00589 |
| PSt | Partition coefficient - stomach | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00590 |
| PSI | Partition coefficient - small intestine | dimensionless | not specified |
| PRest | Partition coefficient - rest of body | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00585 |
| kabs | Uptake from GI | /h | not specified |
| CLint | Hepatic intrinsic clearance | L/h | http://purl.obolibrary.org/obo/PBPKO_00234 |
| CIL | Concentration in GI lumen | mg/L | http://purl.obolibrary.org/obo/PBPKO_00538 |
| CSI | Concentration in small intestine | mg/L | not specified |
| CSpleen | Concentration in spleen | mg/L | not specified |
| CSt | Concentration in stomach | 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 |
| Met | Hepatic metabolism - intrinsic clearance | dimensionless | not specified |