Ou 2018
Notes
Hg PBK (Ou et al., 2018):
Overview
| key | value |
|---|---|
| Modelled species/orgamism(s) | http://purl.obolibrary.org/obo/NCBITaxon_9606 |
| Model chemical(s) | http://purl.obolibrary.org/obo/CHEBI_25322 |
| Input route(s) | 1 (oral) |
| Time resolution | h |
| Amounts unit | ug |
| Volume unit | L |
| Number of compartments | 7 |
| Number of species | 9 |
| Number of parameters | 42 (20 external / 22 internal) |
Diagram
Compartments
| id | name | unit | model qualifier |
|---|---|---|---|
| Gut_lumen | Gut lumen compartment | L | http://purl.obolibrary.org/obo/PBPKO_00478 |
| Gut | Gut compartment | L | http://purl.obolibrary.org/obo/PBPKO_00477 |
| Liver | Liver compartment | L | http://purl.obolibrary.org/obo/PBPKO_00558 |
| Red_Blood_Cell | Red blood cells compartment | L | http://purl.obolibrary.org/obo/PBPKO_00634 |
| Plasma | Plasma compartment | L | http://purl.obolibrary.org/obo/PBPKO_00488 |
| Rest | Rest of body compartment | L | http://purl.obolibrary.org/obo/PBPKO_00450 |
| Feces | Feces compartment | L | http://purl.obolibrary.org/obo/PBPKO_00555 |
Species
| id | name | unit | model qualifier |
|---|---|---|---|
| AGut_lumen | Amount in gut lumen | ug | not specified |
| AGut | Amount in gut | ug | http://purl.obolibrary.org/obo/PBPKO_00496 |
| ALiver | Amount in liver | ug | http://purl.obolibrary.org/obo/PBPKO_00497 |
| ARBC | Amount in red blood cells | ug | http://purl.obolibrary.org/obo/PBPKO_00623 |
| APlasma | Amount in plasma | ug | http://purl.obolibrary.org/obo/PBPKO_00502 |
| ARest | Amount in rest of body | ug | http://purl.obolibrary.org/obo/PBPKO_00501 |
| AFeces | Amount in feces | ug | http://purl.obolibrary.org/obo/PBPKO_00273 |
| ALiver_Met | Amount in liver (metabolised) | ug | http://purl.obolibrary.org/obo/PBPKO_00497 |
| AGutlumen_Met | Amount in gut lumen (metabolised) | ug | not specified |
Transfer equations
| id | from | to | equation |
|---|---|---|---|
| _J0 | AGut_lumen | AGut | kabs * CGut_lumen * Frac |
| _J1 | AGut | ALiver | QGI * CGI / PGI |
| _J2 | APlasma | AGut | QGI * CPlasma |
| _J3 | APlasma | ALiver | QL * CPlasma |
| _J4 | ALiver | APlasma | (QL + QGI) * CLiver / PL |
| _J5 | APlasma | ARest | QRest * CPlasma |
| _J6 | ARest | APlasma | QRest * CRest / PRest |
| _J7 | APlasma | ARBC | CPlasma * Qrbc |
| _J8 | ARBC | APlasma | Qrbc * CRBC / PRBC |
| _J9 | ALiver | AGut_lumen | kbiliary * CLiver |
| _J10 | ALiver | ALiver_Met | kmet_liver * CLiver |
| _J11 | AGut_lumen | AGutlumen_Met | kmet_gutlumen * CGut_lumen |
| _J12 | AGut_lumen | AFeces | kfe * CGut_lumen |
ODEs
\(\frac{d[\mathtt{AGut-lumen}]}{dt} = - \mathit{kabs}\cdot \mathit{CGut_{lumen}}\cdot \mathit{Frac} + \mathit{kbiliary}\cdot \mathit{CLiver} - \mathit{kmet_{gutlumen}}\cdot \mathit{CGut_{lumen}} - \mathit{kfe}\cdot \mathit{CGut_{lumen}}\)
\(\frac{d[\mathtt{AGut}]}{dt} = \mathit{kabs}\cdot \mathit{CGut_{lumen}}\cdot \mathit{Frac} - \frac{\mathit{QGI}\cdot \mathit{CGI}}{\mathit{PGI}} + \mathit{QGI}\cdot \mathit{CPlasma}\)
\(\frac{d[\mathtt{ALiver}]}{dt} = \frac{\mathit{QGI}\cdot \mathit{CGI}}{\mathit{PGI}} + \mathit{QL}\cdot \mathit{CPlasma} - \frac{(\mathit{QL}+\mathit{QGI})\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{kbiliary}\cdot \mathit{CLiver} - \mathit{kmet_{liver}}\cdot \mathit{CLiver}\)
\(\frac{d[\mathtt{ARBC}]}{dt} = \mathit{CPlasma}\cdot \mathit{Qrbc} - \frac{\mathit{Qrbc}\cdot \mathit{CRBC}}{\mathit{PRBC}}\)
\(\frac{d[\mathtt{APlasma}]}{dt} = - \mathit{QGI}\cdot \mathit{CPlasma} - \mathit{QL}\cdot \mathit{CPlasma} + \frac{(\mathit{QL}+\mathit{QGI})\cdot \mathit{CLiver}}{\mathit{PL}} - \mathit{QRest}\cdot \mathit{CPlasma} + \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}} - \mathit{CPlasma}\cdot \mathit{Qrbc} + \frac{\mathit{Qrbc}\cdot \mathit{CRBC}}{\mathit{PRBC}}\)
\(\frac{d[\mathtt{ARest}]}{dt} = \mathit{QRest}\cdot \mathit{CPlasma} - \frac{\mathit{QRest}\cdot \mathit{CRest}}{\mathit{PRest}}\)
\(\frac{d[\mathtt{AFeces}]}{dt} = \mathit{kfe}\cdot \mathit{CGut_{lumen}}\)
\(\frac{d[\mathtt{ALiver-Met}]}{dt} = \mathit{kmet_{liver}}\cdot \mathit{CLiver}\)
\(\frac{d[\mathtt{AGutlumen-Met}]}{dt} = \mathit{kmet_{gutlumen}}\cdot \mathit{CGut_{lumen}}\)
Assignment rules
| variable | assignment |
|---|---|
| VGut_lumen | VGut_lumenc * BW |
| VG | VGc * BW |
| VL | VLc * BW |
| VRBC | VRBCc * BW |
| VPlasma | VPlasmac * BW |
| VRest | BW - VGut_lumen - VG - VL - VRBC - VPlasma |
| QC | 20 * pow(BW, 0.75) |
| QGI | QGc * BW |
| QL | QLc * QC |
| QRest | QC - QL - QGI |
| Qrbc | Qrbcc * pow(BW, 0.75) |
| kabs | kabsc * pow(BW, 0.75) |
| kfe | kfec * pow(BW, 0.75) |
| kmet_gutlumen | kmet_gutlumenc * pow(BW, 0.75) |
| kmet_liver | kmet_liverc * pow(BW, 0.75) |
| kbiliary | kbiliaryc * pow(BW, 0.75) |
| CGut_lumen | AGut_lumen / Gut_lumen |
| CGI | AGut / Gut |
| CLiver | ALiver / Liver |
| CRBC | ARBC / Red_Blood_Cell |
| CPlasma | APlasma / Plasma |
| CRest | ARest / Rest |
Initial assignments
| variable | assignment |
|---|---|
| Gut_lumen | VGut_lumen |
| Gut | VG |
| Liver | VL |
| Red_Blood_Cell | VRBC |
| Plasma | VPlasma |
| Rest | VRest |
Parameters
| id | name | unit | model qualifier |
|---|---|---|---|
| Age | Age | y | http://purl.obolibrary.org/obo/PBPKO_00521 |
| BW | Bodyweight | kg | http://purl.obolibrary.org/obo/PBPKO_00008 |
| VGut_lumenc | Volume fraction of gut lumen | dimensionless | not specified |
| VGc | Volume fraction of gut | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00509 |
| VLc | Volume fraction of liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00078 |
| VRBCc | Volume fraction of red blood cells | dimensionless | not specified |
| VPlasmac | Volume fraction of plasma | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00104 |
| VGut_lumen | Volume of gut lumen | L | not specified |
| VG | Volume of gut | L | http://purl.obolibrary.org/obo/PBPKO_00524 |
| VL | Volume of liver | L | http://purl.obolibrary.org/obo/PBPKO_00077 |
| VRBC | Volume of red blood cells | L | http://purl.obolibrary.org/obo/PBPKO_00108 |
| VPlasma | Volume of plasma | L | http://purl.obolibrary.org/obo/PBPKO_00103 |
| VRest | Volume of rest of body | L | http://purl.obolibrary.org/obo/PBPKO_00105 |
| QC | Cardiac output | not specified | http://purl.obolibrary.org/obo/PBPKO_00013 |
| QLc | Cardiac output to liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00025 |
| QGc | Cardiac output fraction to gut | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00513 |
| Qrbcc | Maternal red cells / plasma diffusion | dimensionless | not specified |
| QGI | Blood flow to gut | L/h | http://purl.obolibrary.org/obo/PBPKO_00531 |
| QL | Blood flow to liver | L/h | http://purl.obolibrary.org/obo/PBPKO_00024 |
| QRest | Blood flow to rest of body | L/h | http://purl.obolibrary.org/obo/PBPKO_00050 |
| Qrbc | Maternal red cells / plasma diffusion | L/h | not specified |
| kabsc | Reabsorption rate in gut | dimensionless | not specified |
| kabs | Reabsorption rate in gut | dimensionless | not specified |
| Frac | not specified | not specified | not specified |
| PGI | Partition coefficient blood-gut | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00572 |
| PL | Partition coefficient blood-liver | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00577 |
| PRBC | Partition coefficient red blood cells | dimensionless | not specified |
| PRest | Partition coefficient blood- rest body | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00585 |
| kfec | fecal elimination rate | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00236 |
| kfe | fecal elimination rate | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00230 |
| kmet_gutlumenc | Metabolism rate constant in gut | dimensionless | not specified |
| kmet_gutlumen | Metabolism rate in gut | dimensionless | not specified |
| kmet_liverc | metabolism rate constant in liver | dimensionless | not specified |
| kmet_liver | metabolism rate in liver | dimensionless | not specified |
| kbiliaryc | Biliary clearance | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00233 |
| kbiliary | Biliary clearance | dimensionless | http://purl.obolibrary.org/obo/PBPKO_00233 |
| CGut_lumen | Concentration in gut lumen | ug/L | not specified |
| CGI | Concentration in gut | ug/L | http://purl.obolibrary.org/obo/PBPKO_00538 |
| CLiver | Concentration in liver | ug/L | http://purl.obolibrary.org/obo/PBPKO_00539 |
| CRBC | Concentration in red blood cells | ug/L | http://purl.obolibrary.org/obo/PBPKO_00301 |
| CPlasma | 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 |