Deepika
Notes
PFOS PBK Deepika et al. 2021. Equations are built up as represented in the schema as code is unavailable. Used values from Loccisano PFOA.
Overview
| key | value |
|---|---|
| Modelled species/orgamism(s) | http://purl.obolibrary.org/obo/NCBITaxon_9606 |
| Model chemical(s) | http://purl.obolibrary.org/obo/CHEBI_39421 |
| Input route(s) | 1 (oral) |
| Time resolution | d |
| Amounts unit | ug |
| Volume unit | L |
| Number of compartments | 4 |
| Number of species | 4 |
| Number of parameters | 25 (11 external / 14 internal) |
Diagram
Compartments
| id | name | unit | model qualifier |
|---|---|---|---|
| GI | Gastrointestinal tract | L | http://purl.obolibrary.org/obo/PBPKO_00477 |
| Liver | Liver | L | http://purl.obolibrary.org/obo/PBPKO_00558 |
| Plasma | Plasma | L | http://purl.obolibrary.org/obo/PBPKO_00488 |
| Rest | Rest of the body | L | http://purl.obolibrary.org/obo/PBPKO_00450 |
Species
| id | name | unit | model qualifier |
|---|---|---|---|
| AGI | Amount in gastrointestinal tract | ug | http://purl.obolibrary.org/obo/PBPKO_00496 |
| ALiver | Amount in liver | ug | http://purl.obolibrary.org/obo/PBPKO_00497 |
| APlasma | Amount in plasma | ug | http://purl.obolibrary.org/obo/PBPKO_00502 |
| ARest | Amount in the rest of the body | ug | http://purl.obolibrary.org/obo/PBPKO_00501 |
Transfer equations
| id | from | to | equation |
|---|---|---|---|
| _J0 | APlasma | AGI | QG * Free * CPlasmaTotal |
| _J1 | AGI | APlasma | QG * Free * CGI / PG |
| _J2 | APlasma | ALiver | QL * Free * CPlasmaTotal |
| _J3 | ALiver | APlasma | (QL + QG) * Free * CLiver / PL |
| _J4 | APlasma | ARest | QRest * Free * CPlasmaTotal |
| _J5 | ARest | APlasma | QRest * Free * CRest / PRest |
ODEs
\(\frac{d[\mathtt{AGI}]}{dt} = \mathit{QG}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} - \frac{\mathit{QG}\cdot \mathit{Free}\cdot \mathit{CGI}}{\mathit{PG}}\)
\(\frac{d[\mathtt{ALiver}]}{dt} = \mathit{QL}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} - \frac{(\mathit{QL}+\mathit{QG})\cdot \mathit{Free}\cdot \mathit{CLiver}}{\mathit{PL}}\)
\(\frac{d[\mathtt{APlasma}]}{dt} = - \mathit{QG}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} + \frac{\mathit{QG}\cdot \mathit{Free}\cdot \mathit{CGI}}{\mathit{PG}} - \mathit{QL}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} + \frac{(\mathit{QL}+\mathit{QG})\cdot \mathit{Free}\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{QRest}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} + \frac{\mathit{QRest}\cdot \mathit{Free}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{ARest}]}{dt} = \mathit{QRest}\cdot \mathit{Free}\cdot \mathit{CPlasmaTotal} - \frac{\mathit{QRest}\cdot \mathit{Free}\cdot \mathit{CRest}}{\mathit{PRest}}\)
Assignment rules
| variable | assignment |
|---|---|
| GI | VG |
| Liver | VL |
| Plasma | VPlasma |
| Rest | VRest |
| VL | VLc * BW |
| VPlasma | VPlasmac * BW |
| VG | VGc * BW |
| VRest | 0.84 * BW - VL - VPlasma - VG |
| QC | 12.5 * pow(BW, 0.75) |
| QPlasma | QC * (1 - Htc) |
| QL | QLc * QPlasma |
| QG | QGc * QPlasma |
| QRest | QPlasma - QL - QG |
| CGI | AGI / GI |
| CLiver | ALiver / Liver |
| CPlasma | APlasma / Plasma |
| CPlasmaTotal | CPlasma / Free |
| CRest | ARest / Rest |
Parameters
| id | name | unit | model qualifier |
|---|---|---|---|
| BW | bodyweight | kg | http://purl.obolibrary.org/obo/PBPKO_00008 |
| VLc | Volume fraction of liver | L/kg | http://purl.obolibrary.org/obo/PBPKO_00078 |
| VPlasmac | Volume fraction of plasma | L/kg | http://purl.obolibrary.org/obo/PBPKO_00104 |
| VGc | Volume fraction of gut | L/kg | http://purl.obolibrary.org/obo/PBPKO_00509 |
| VL | Liver volume | L | http://purl.obolibrary.org/obo/PBPKO_00077 |
| VPlasma | Volume of plasma | L | http://purl.obolibrary.org/obo/PBPKO_00103 |
| VG | Volume of the gut | L | http://purl.obolibrary.org/obo/PBPKO_00524 |
| VRest | Volume of the rest of the body | L | http://purl.obolibrary.org/obo/PBPKO_00105 |
| QC | Cardiac output | L/d | http://purl.obolibrary.org/obo/PBPKO_00013 |
| QPlasma | Cardiac output of plasma | L/d | http://purl.obolibrary.org/obo/PBPKO_00528 |
| Htc | Hematocrit | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00527 |
| QLc | Fraction of blood flow to liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00025 |
| QGc | Fraction of blood flow to gut | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00513 |
| QL | Liver blood flow | L/d | http://purl.obolibrary.org/obo/PBPKO_00024 |
| QG | Gut blood flow | L/d | http://purl.obolibrary.org/obo/PBPKO_00531 |
| QRest | Blood flow to the rest of the body | L/d | http://purl.obolibrary.org/obo/PBPKO_00050 |
| Free | Unbound fraction | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00149 |
| PL | Liver to plasma partition coefficient | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00170 |
| PG | Gut to plasma partition coefficient | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00166 |
| PRest | Rest of body to plasma partition coefficient | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00518 |
| CGI | Concentration in gastrointestinal tract | ug/L | http://purl.obolibrary.org/obo/PBPKO_00538 |
| CLiver | Concentration in liver | ug/L | http://purl.obolibrary.org/obo/PBPKO_00539 |
| CPlasma | Unbound concentration in plasma | ug/L | not specified |
| CPlasmaTotal | Total concentration in plasma | ug/L | http://purl.obolibrary.org/obo/PBPKO_00549 |
| CRest | Concentration in rest of body | ug/L | http://purl.obolibrary.org/obo/PBPKO_00548 |