pbpk ids and data¶
The id scheme, the annotation, the values with provenance, the data files and the units of the PBPK library, see Annotation.
ids¶
The id scheme of the PBPK models.
Every id of a generated model is built here, so that the organs, the
observers and the fits agree on them. A flat id is <ORGAN>__<local id>
(LI__Cpl_api), the ids of substances are suffixed by _<substance>.
module-attribute
¶
The cardiac output without impairment, of which the organ flows are fractions.
module-attribute
¶
The glomerular filtration rate at renal function 1, of which the renal function is the factor.
module-attribute
¶
The scaling factor of the lean tissues, the blood and the cardiac output.
module-attribute
¶
The renal function relative to normal.
module-attribute
¶
The cardiac function (cardiac output) relative to normal.
module-attribute
¶
The portosystemic shunt: the fraction of the liver inflow which bypasses the liver.
module-attribute
¶
The functional fraction of the liver tissue.
module-attribute
¶
The share of the tubular capacity of the kidney which follows the renal function.
module-attribute
¶
The severity of liver cirrhosis: 0 healthy, 1, 2, 3 the Child-Pugh classes A, B, C.
module-attribute
¶
The severity of heart failure: 0 healthy, 1 to 4 the NYHA classes I to IV.
module-attribute
¶
The switch (0 off, 1 on) of the hepatic changes of chronic kidney disease.
module-attribute
¶
The GFR per 1.73 m2 body surface area of the renal function, which gives the CKD stage.
module-attribute
¶
The volume fraction of a zone of a zonated organ, 1/n of n zones.
module-attribute
¶
The local volume of the single intestinal lumen, the compartment of Clumen_<s>.
module-attribute
¶
The rate of the transit of the bile into the intestinal lumen.
module-attribute
¶
The local transit time of the single intestinal lumen into the feces.
module-attribute
¶
The prandial state, 0 fasted (default) and 1 fed: it slows the gastric emptying.
module-attribute
¶
The id of the submodel of the intestine (the small intestine, or the
segmented and single lumen intestine, which replace small and large
intestine), the prefix of the hand-written models GU__.
module-attribute
¶
The local volume of the intestine which replaces small and large intestine, Vsi + Vla.
module-attribute
¶
The local vascular fraction of the intestine of small and large intestine.
module-attribute
¶
The local interstitial fraction of the intestine of small and large intestine.
module-attribute
¶
The local blood flow of the intestine of small and large intestine, Qsi + Qla.
module-attribute
¶
The local blood flow of the intestinal wall past the mucosa, Qgu - Qmu_total.
module-attribute
¶
The local blood flow of the mucosa of all segments.
module-attribute
¶
The local volume of the mucosa of all segments.
module-attribute
¶
The local fraction of the intestinal tissue without the mucosa, 1 - Vmu_total/Vti.
module-attribute
¶
The local fraction of the intestinal tissue which is mucosa.
module-attribute
¶
The local fraction of the intestinal blood flow which perfuses the mucosa.
module-attribute
¶
The local transit time of the stomach in the fed state.
module-attribute
¶
The transit time of the stomach which the transit of the stomach reads: of
the prandial state (FED, T_st fasted to T_st_fed fed) times the factor
of the gastric emptying of chronic kidney disease, a constant of the segmented
intestine and its output, an id of the top model (min).
module-attribute
¶
GUT_SEGMENTS = (
"st",
"du",
"jej1",
"jej2",
"ile1",
"ile2",
"cae",
"asc",
"tra",
"des",
"sig",
"rec",
)
The lumen segments of the segmented intestine, in the order of the transit: stomach, duodenum, upper and lower jejunum, upper and lower ileum, caecum, colon ascendens, transversum, descendens, sigmoid and rectum.
module-attribute
¶
The tubule segments of the nephron kidney, in the order of the tubular flow: proximal tubule, loop of Henle, distal tubule and collecting duct.
module-attribute
¶
The local id of the exchange between plasma and interstitium of an organ.
The id of the factor of all impairments on a quantity, fimp_GFR.
The product of the factors of the conditions (Child-Pugh, chronic kidney
disease, heart failure) on the quantity pid of the body.
The id of the factor of one condition, fcp_albumin, fckd_hematocrit.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
condition
|
str
|
the condition, |
required |
key
|
str
|
the key of the factor in |
required |
The id of the factor of the impairments on the activity of a protein in an organ.
In the organ the local input fimp_cyp3a4, in the body fimp_li_cyp3a4;
the rates of the protein in the organ run with f_<protein> times it, so
that a genotype or an interaction which sets LI__f_cyp3a4 acts on top
of the impairment.
The id of the submodel of an organ, the organ id in capitals, LI.
The small intestine is the submodel GU (gut) for every intestine
variant: the segmented and the single lumen intestine replace small and
large intestine with it; with the standard organs as intestine the small
intestine is GU and the large intestine LA.
The local id of a compartment of an organ, Vpl; of a zone Vpl_z1.
The local id of a species of substance s in a part, Cpl_<s>; of a zone Cpl_z1_<s>.
The id of a species in a blood pool, Cve_<s> (plasma), Cve_bc_<s> (blood cells).
The id of the blood flow of an organ as fraction of cardiac output, fQli.
The id of the volume of a blood pool as fraction of the blood volume, fVve.
The id of the compartment of a pool species of s with erythrocytes in equilibrium.
The pool volume times the blood to plasma ratio, Vve_pl_<s>: the plasma
species then holds the amount of the blood.
The local id of the compartment of Cpl_<s> with erythrocytes in equilibrium.
The vascular volume of the organ times the blood to plasma ratio,
Vpl_<s> (of a zone Vpl_z1_<s>): the plasma species then holds the
amount of the blood.
The id of the vascular fraction of the organ volume, f_vas_li.
The id of the interstitial fraction of the organ volume, f_int_li.
The id of the reference tissue volume of the organs s enters, Vti_total_ref_<s>.
The tissue volume of the reference individual summed over the organs
whose exchange is a share of ftissue_<s>; the exchange of an organ is
ftissue_<s> * Vti_o / Vti_total_ref_<s>, so it scales with the individual.
The local id of the exchange of the whole healthy liver, PS_ref_<s>.
The exchange of the whole liver in l/min (ps with
ps_per_volume=False): the liver has PS_<s> = PS_ref_<s> * f_functional.
The local id of the exchange of s per litre of organ, kps_<s>.
The exchange of an organ given per litre of organ (ps of the
distribution with ps_per_volume, 1/min): the organ has
PS_<s> = kps_<s> * V<o>.
The local id of the slow pool of s in the tissue of an organ, Cslow_<s>.
A concentration in the tissue compartment Vti (SlowPool), exposed to
the observers as C<o>_slow_<s> (organ_species).
The id of the exchange of the slow pool of s per litre of tissue, kslow_<s> (1/min).
The local id of the exchange of s between the tissue and its slow pool, J_slow_<s>.
The id of the plasma concentration leaving an organ, Cout_li_<s>.
The id of the top model of an element of an organ which a PD component or an observer reads.
The organ exposes the element as an output, which replaces this parameter
of the top model: the organ token follows the prefix of the local id. A
concentration C<part>_<s> is C<o>_<part>_<s>, Cli_ic_api for the
cells of the liver (LI__Cic_api in the flat model); an unbound
concentration Cu_<part>_<s> is Cu_<o>_<part>_<s> (Cu_li_ic_api), the
one spelling of the unbound concentration of an organ (the pools keep
theirs, C<pool>_free_<s>); an amount A<x> is A<o>_<x>
(Asi_solid_du_api).
Raises:
| Type | Description |
|---|---|
ValueError
|
if the local id is no concentration |
The id of the blood cell concentration leaving an organ, Cout_li_bc_<s>.
Only for a substance with kinetic blood cells.
The local id of the inflow of s from a pool into an organ, J_in_ar_pl_<s>.
part is the part of the blood which carries it, plasma or blood cells.
The local id of the outflow of s from an organ into its pool, J_out_pl_<s>.
The local id of the shunt of s from a pool past the liver, J_shunt_po_pl_<s>.
part is the part of the blood which carries it, plasma or blood cells.
The local id of the glomerular filtration of s into the urine, J_gfr_<s>.
The local id of the passive exchange of s into a part of an organ, J_ti_<s>.
From plasma into the tissue, the interstitium or the blood cells, from
the interstitium into the cells (J_ic_<s>); in a zone J_ti_z1_<s>.
The local id of the flow of s from a zone into the next one, J_sin_z1_pl_<s>.
part is the part of the blood which carries it, plasma or blood cells
(the whole organ of a flow-limited substance carries it as plasma).
The local id of the blood cell concentration leaving an organ, Cout_bc_<s>.
The id of the plasma concentration of an endogenous substance at the start, baseline_<s>.
The id of the exchange rate between plasma and blood cells, kex_bc_<s>.
The id of the fraction of the filtrate which is reabsorbed, f_reabsorbed_<s>.
The id of the renal threshold of a saturable reabsorption (mM), reab_threshold_<s>.
The id of the sharpness of the threshold of a saturable reabsorption, reab_n_<s>.
The id of the urinary excretion rate, Rurine_<s> (mmole/min).
The sum of the fluxes of the kidney into the urine Aurine_<s>, an output
of the kidney which replaces the parameter of the top model.
The id of the fecal excretion rate, Rfeces_<s> (mmole/min).
A readout of the intestine (PBPKDefinition.readouts): the net flux of
the reactions of the intestine into the feces Afeces_<s>, an output of
the intestine which replaces the parameter of the top model.
The id of the dissolved amount of s in the intestinal lumen, Alumen_<s> (mmole).
A readout of the intestine (PBPKDefinition.readouts): the sum over the
lumen segments of Vlumen_<seg>*Clumen_<seg>_<s>, an output of the
intestine; the undissolved drug of a tablet is not in it.
The id of the absorption rate of s, Rabs_<s> (mmole/min).
A readout of the intestine (PBPKDefinition.readouts): the sum of the
fluxes from the lumen into the intestinal wall (the mucosa, else the
wall), the absorption of every segment and an apical influx; not the
absorption rate constant ka_<s> (absorption).
The id of the amount of s absorbed from the lumen, Aabs_<s> (mmole).
A readout of the intestine (PBPKDefinition.readouts): the integral of
the absorption rate Rabs_<s> (the fluxes from the lumen into the wall,
an apical influx included) since the start, a state of the intestine.
The id of the gross absorbed fraction of the oral dose of s, Fa_<s>.
A readout of the intestine (PBPKDefinition.readouts): the absorbed
amount Aabs_<s> over the oral dose given until then (tablet and
solution, mmole), 0 before a dose; gross, before the first pass of the
wall and the liver, so above the bioavailability.
The local id of the oral dose of s which the intestine has applied, Aapp_<s> (mmole).
The integral of the outflows of the oral dose states (dissolution and
emptying of a tablet, the application of a solution), a state of the
intestine which Fa_<s> reads: with the dose states it is the oral dose
given, also over several doses.
The id of the efflux rate of s into the intestinal lumen, Reff_<s> (mmole/min).
A readout of the intestine (PBPKDefinition.readouts): the sum of the
fluxes from the intestinal wall into the lumen, the apical efflux of
every segment.
The local id of the concentration in an intestinal lumen segment, Clumen_du_<s>.
Without a segment the single lumen, Clumen_<s>.
The local id of the volume of a lumen segment, Vlumen_du (single: Vlumen).
The local id of the undissolved amount of s in a lumen segment, Asolid_du_<s>.
In the stomach (and the single lumen) the dose state PODOSE_<s> is the
undissolved drug.
The local id of the concentration in the lumen of a tubule segment, Ctub_pt_<s>.
The segment is always part of the id (TUBULE_SEGMENTS), so the id
names its substance without ambiguity.
The local id of the volume of the lumen of a tubule segment, Vtub_pt.
The local id of the tubular flow leaving a segment as fraction of the GFR, f_tub_pt.
The local id of the tubular flow of s out of a segment, J_tub_pt_<s>.
Out of the collecting duct the urinary excretion J_tub_cd_<s>.
The local id of the reabsorbed fraction of s out of the collecting duct, J_reab_<s>.
The local id of the concentration in the mucosa of a segment, Cmu_du_<s>.
The local id of the unbound concentration in the mucosa of a segment, Cu_mu_du_<s>.
The local id of a tissue compartment of the intestinal wall without the mucosa, Vti_wall.
The compartment of the tissue species of a substance with mucosa species: the mucosa is carved out of the wall, so the capacity of the intestine stays that of the wall without mucosa.
The local id of the volume of the mucosa of a segment, Vmu_du.
The local id of the blood flow of the mucosa of a segment, Qmu_du.
The local id of the mucosa to plasma coefficient, K_mu_<s>.
The local id of the transit time of a lumen segment, T_du (single: t_lumen).
The local id of the absorption scaling of a lumen segment, f_area_du.
The id of the fraction of the absorbed flux entering the body, fabs_<s>.
The id of the factor of the absorption in the large intestine, f_ka_colon_<s>.
Of the segmented intestine: scales ka_<s>*f_area_<seg> of the segments
of the large intestine.
The id of the factor of the absorption of s in a lumen segment, f_ka_<seg>_<s>.
Of the regional absorption profile of the segmented intestine
(RegionalAbsorption): scales ka_<s>*f_area_<seg> of the segment.
The id of the rate constant of a conversion in the lumen (1/hr), kconv_<s>_<m>.
Of a LumenConversion of the segmented intestine, a parameter of the
top model: the substrate <s> converts into the product <m> with
kconv/60*V*C in every segment of the conversion.
The local id of a conversion in a lumen segment, J_conv_<seg>_<s>_<m>.
The local id of the transit of s out of a lumen segment, J_tr_du_<s>.
The undissolved drug J_trs_du_<s>.
The local id of the dissolution of s in a lumen segment, J_dis_du_<s>.
The local id of a flow of the mucosa of a segment, J_mu_in_du_<s>.
kind is in (arterial inflow), out (outflow into the portal vein)
or bc (the blood cells of the mucosal blood, which pass it).
The local id of the share of a process in a segment or a zone, w_cyp3a4_du.
key is the protein (or profile) in lower case or uniform (by mucosa
volume); in the zone of a zonated organ w_cyp3a4_z1.
The local id of the relative abundance of a profile in a zone, p_cyp3a4_z1.
The local id of a process of the chemistry in a segment or a zone, CYP3A4_DRG_du.
In the mucosa of a segment of the intestine or a zone of a zonated organ
(CYP3A4_DRG_z1).
The local id of the ratio of a constant of a process to another, <p>_Vmax_ratio.
The factor of RateOf: the constant <p>_Vmax (or <p>_k) of the
process is this ratio times the constant of the other process of the
organ.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
process
|
str
|
the id of the process. |
required |
constant
|
str
|
the constant, |
required |
The local id of the fraction of a metabolism which forms a product, f_<p>_<s>.
A constant of the organ when the fractions of the metabolism are values
or the remainder REST, which is 1 - sum of the others.
The local id of the formation of a product of a metabolism, <p>_to_<s>.
The reaction of a metabolism with product fractions as constants forms
the product with its fraction of the rate of the metabolism,
f_<p>_<s> * <p> (in a zone or a segment <p>_to_<s>_<zone>).
The local id of the dissolution rate of a tablet (1/min), kdis_<s>.
An assignment rule of the intestine for a Weibull or dose-dependent
dissolution; a first order dissolution is the constant Ka_dis_<s>.
The local id of the mean age of the undissolved dose (min), age_dis_<s>.
The local id of the age-weighted undissolved amount (mmole*min), W_dis_<s>.
The state whose ratio to the undissolved amount is the mean time since
the dose (age_dis_<s>) of a Weibull dissolution.
The id of the factor of the dissolution rate in the fed state, f_dis_fed_<s>.
The id of the factor of a modified-release formulation, f_dis_release_<s>.
The id of the time of half dissolution of a Weibull dissolution (min), t50_dis_<s>.
The id of the shape of a Weibull dissolution, shape_dis_<s>.
The id of the lag time of a Weibull dissolution (min), lag_dis_<s>.
The id of the undissolved amount of half the dissolution rate (mg), D50_dis_<s>.
The id of the rate of the absorption from the intestinal lumen, ka_<s>.
The first order absorption of the single lumen; in the segmented intestine the absorption rate constant of the small intestine, which the area factor of a segment scales.
The id of the application of a dose state, J_iv_<s>, J_po_<s>, J_sol_<s>.
The local id of the absorption from a lumen segment, J_abs_du_<s>.
The local id of the unabsorbed fraction of the absorption into the feces, J_feces_du_<s>.
Of a lumen segment with fabs_<s>, J_feces_<s> of the single lumen.
The id of the transit of the bile into the intestinal lumen, J_bile_<s>.
Into the feces when the intestine has no lumen (standard organs).
The id of the exchange of s between plasma and blood cells of a pool, J_bc_ve_<s>.
The id of the weight of an organ outflow or a pool in the arm vein, w_arm_sk.
The id of the unbound concentration in the hepatic vein, Chv_free_<s>.
The id of the blood concentration in the hepatic vein, Chv_blood_<s>.
The local id of the unbound concentration of s in a tissue part, Cu_ti_<s>.
In a zone of a zonated organ Cu_ti_z1_<s>.
The id of the base activity of a protein in an organ, f_cyp3a4.
A constant of every organ in which a process uses the protein (flat
LI__f_cyp3a4), relative to normal (1): the factor which genotype,
impairment and the experiments set. Interactions act on top of it, not on
it: mechanism-based inhibition and induction through the turnover state
E_<protein> of the organ, reversible inhibition through the inhibitor
terms in the rate of every process of the protein. A process of the
protein runs with f_<protein> (times E_<protein>) on its Vmax or
clearance.
The id of the turnover state of a protein in an organ, E_cyp3a4.
The amount of the protein relative to its baseline (initially 1), a state of the organs with a process of the protein when a substance of the definition inactivates (mechanism-based) or induces it.
The id of the inhibition constant of s on a protein, Ki_cyp3a4_<s>.
The competitive constant of a mixed inhibition, the KI (half-maximal inactivation) of a mechanism-based inhibition.
The id of the maximal inactivation rate of s on a protein, kinact_cyp3a4_<s>.
The flat species ids of substance s, by the id scheme.
Only species of exactly this substance match: api does not match the
species of api_m2, drg not those of xdrg.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
s
|
str
|
the substance id. |
required |
ids
|
Iterable[str]
|
the ids to select from. |
required |
Returns:
| Type | Description |
|---|---|
list[str]
|
The ids which are an organ species (of a zone as well), a slow |
list[str]
|
pool of a tissue, a pool species, a blood cell pool species, a lumen, |
list[str]
|
undissolved or mucosa species, a tubule species of |
list[str]
|
of |
The id of a clearance of the generated steady state, CLss_<s> [l/min].
In an organ (organ None) the clearance of its plasma at the steady state
of s, the declared clearances of its tissue included
(pkpdsim.pbpk.stationary); with organ its output in the top model,
CLss_<o>_<s>. In the top model CLss_<s> is the clearance of the
arterial plasma by the body at the steady state (without the organ of a
saturable process), of a substance whose baseline the library solves.
The id of a net source of the generated steady state, Rss_<s> [mmole/min].
In an organ the net source into its plasma at the steady state of s
(the declared rates of plasma and tissue), with organ its output in
the top model, Rss_<o>_<s>; in the top model Rss_<s> is the net
source of the body at the steady state (without the organ of a saturable
process), see steady_clearance.
The id of the capacity of a saturable process at the steady state, Vss_<s> [mmole/min].
In an organ, with organ its output in the top model Vss_<o>_<s>.
The id of the Michaelis constant of a saturable process at the steady state, Kss_<s> [mM].
In an organ, with organ its output in the top model Kss_<o>_<s>.
The id of the plasma of the organ of a saturable process at the steady state, Css_<o>_<s> [mM].
A parameter of the top model, the root of the quadratic of the steady state of a substance whose baseline the library solves.
The id of the base of a delta, <sid>_0: the value of an observer at the start.
The constant which <sid>_delta subtracts (PBPKDefinition.deltas). It
is no start of a species (PBPKDefinition.starts): the word "start" of
the library names the initial concentrations of the species only.
annotation¶
The annotation of every element the library creates (#63).
Every generator annotates an element when it creates it, with
annotate(element, kind, ...): the kind names what the element is (an organ
volume, the plasma of an organ, a metabolism) and selects one row of the
table KINDS, which holds its SBO term and its ontology terms. The context
of the element adds the terms of where it is: the organ (UBERON and the
compartment terms of pkpdsim.annotations, the PBPKO compartment), the
blood pool, the lumen segment, the protein of a process (UniProt, NCIT) and
the substance of a species (the annotations of its specification).
The PBPKO terms are those of the pinned pymetadata (PBPKO): a kind gives
its PBPKO term, and an organ-specific term (VOLUME_OF_LIVER) where PBPKO
has one for the organ. Where PBPKO has no term, the kind takes the nearest
broader PBPKO term and names the missing one (requested); every missing
term is listed in docs/pbpk/annotation.md ("terms requested upstream",
requested_terms).
Every resource is written in one format, the identifiers.org
collection/term of pkpdsim.annotations: pbpko/PBPKO:00558,
uberon/UBERON:0002107, uniprot/P08684.
The qualifiers: BQB.IS for what the element is (the PBPKO term, the kind's
terms, the protein of a process, the substance of a species); the location
is BQB.IS_PART_OF for a compartment, BQB.IS_PROPERTY_OF for a parameter
and BQB.OCCURS_IN for a reaction; a parameter of a protein (activity,
inhibition constant) is BQB.IS_PROPERTY_OF the protein.
module-attribute
¶
The prefix of the resources of PBPKO terms, https://bioregistry.io/PBPKO:00558.
module-attribute
¶
An annotation: the qualifier and the resource, collection/term.
module-attribute
¶
ORGANS = {
Organ.LUNG: _organ(
"lu", "lung", ("LUNG",), "LUNG_COMPARTMENT"
),
Organ.HEART: _organ(
"he", "heart", ("HEART",), "HEART_COMPARTMENT"
),
Organ.BRAIN: _organ(
"br", "brain", ("BRAIN",), "BRAIN_COMPARTMENT"
),
Organ.LIVER: _organ(
"li", "liver", ("LIVER",), "LIVER_COMPARTMENT"
),
Organ.KIDNEY: _organ(
"ki", "kidney", ("KIDNEY",), "KIDNEY_COMPARTMENT"
),
Organ.STOMACH: _organ(
"stomach",
"stomach",
("STOMACH",),
"STOMACH_COMPARTMENT",
),
Organ.SMALL_INTESTINE: _organ(
"si",
"small intestine",
("SMALL_INTESTINE", "INTESTINE"),
"SMALL_INTESTINE_COMPARTMENT",
),
Organ.LARGE_INTESTINE: _organ(
"la",
"large intestine",
("LARGE_INTESTINE", "INTESTINE"),
"LARGE_INTESTINE_COMPARTMENT",
),
Organ.SPLEEN: _organ(
"sp", "spleen", ("SPLEEN",), "SPLEEN_COMPARTMENT"
),
Organ.PANCREAS: _organ(
"pa",
"pancreas",
("PANCREAS",),
"PANCREAS_COMPARTMENT",
),
Organ.MUSCLE: _organ(
"mu", "muscle", ("MUSCLE",), "MUSCLE_COMPARTMENT"
),
Organ.SKIN: _organ(
"sk", "skin", ("SKIN",), "SKIN_COMPARTMENT"
),
Organ.ADIPOSE: _organ(
"ad", "adipose", ("FAT",), "ADIPOSE_COMPARTMENT"
),
Organ.BONE: _organ("bo", "bone", ("BONE",), None),
Organ.GONADS: _organ(
"go", "gonads", ("GONAD",), "GONAD_COMPARTMENT"
),
}
The terms of the organs; the PBPKO token of adipose tissue is FAT, the
intestines take the terms of the intestine where PBPKO has none of their own
(MAXIMUM_RATE_IN_INTESTINE); PBPKO has no compartment of the bone (only of
the bone marrow).
module-attribute
¶
POOLS = {
Pool.ARTERIAL: _Place(
"arterial blood",
(
(BQB.IS_PART_OF, "uberon/UBERON:0013755"),
*_location_terms("ar"),
),
"ARTERIAL_BLOOD_COMPARTMENT",
),
Pool.VENOUS: _Place(
"venous blood",
(
(BQB.IS_PART_OF, "uberon/UBERON:0013756"),
*_location_terms("ve"),
),
"VENOUS_BLOOD_COMPARTMENT",
),
Pool.PORTAL: _Place(
"portal vein blood",
(
(BQB.IS_PART_OF, "uberon/UBERON:0002017"),
*_location_terms("po"),
),
None,
),
}
The terms of the blood pools; PBPKO has no compartment of the portal vein.
module-attribute
¶
SEGMENTS = {
"st": _Place(
"stomach",
tuple(_compartments["stomach"]),
"STOMACH_COMPARTMENT",
),
"du": _Place(
"duodenum",
tuple(_compartments["duodenum"]),
"DUODENUM_COMPARTMENT",
),
"jej1": _Place(
"upper jejunum",
tuple(_compartments["jejunum"]),
"JEJUNUM_COMPARTMENT",
),
"jej2": _Place(
"lower jejunum",
tuple(_compartments["jejunum"]),
"JEJUNUM_COMPARTMENT",
),
"ile1": _Place(
"upper ileum",
tuple(_compartments["ileum"]),
"ILEUM_COMPARTMENT",
),
"ile2": _Place(
"lower ileum",
tuple(_compartments["ileum"]),
"ILEUM_COMPARTMENT",
),
"cae": _Place(
"caecum",
tuple(_compartments["caecum"]),
"CECUM_COMPARTMENT",
),
"asc": _Place(
"ascending colon",
tuple(_compartments["ascending colon"]),
"ASCENDING_COLON_COMPARTMENT",
),
"tra": _Place(
"transverse colon",
tuple(_compartments["transverse colon"]),
"TRANSVERSE_COLON_COMPARTMENT",
),
"des": _Place(
"descending colon",
tuple(_compartments["descending colon"]),
"DESCENDING_COLON_COMPARTMENT",
),
"sig": _Place(
"sigmoid colon",
tuple(_compartments["sigmoid colon"]),
"SIGMOID_COLON_COMPARTMENT",
),
"rec": _Place(
"rectum",
tuple(_compartments["rectum"]),
"RECTUM_COMPARTMENT",
),
"pt": _Place(
"proximal tubule",
tuple(_compartments["proximal tubule"]),
"PROXIMAL_TUBULE_COMPARTMENT",
),
"lh": _Place(
"loop of Henle",
tuple(_compartments["loop of Henle"]),
"LOOP_OF_HENLE_COMPARTMENT",
),
"dt": _Place(
"distal tubule",
tuple(_compartments["distal tubule"]),
"DISTAL_TUBULE_COMPARTMENT",
),
"cd": _Place(
"collecting duct",
tuple(_compartments["collecting duct"]),
"COLLECTING_DUCT_COMPARTMENT",
),
}
The terms of the lumen segments of the intestine and of the tubule of the nephron kidney, by their id token.
module-attribute
¶
SITES = {
"hepatic_vein": _Place(
"hepatic vein",
(
*_location_terms("hv"),
(BQB.IS_PART_OF, "uberon/UBERON:0001143"),
),
None,
),
"arm_vein": _Place(
"arm vein", _location_terms("fov"), None
),
}
The terms of the sampling sites of the observers which are no blood pool.
module-attribute
¶
KINDS = {
"plasma": Kind(
_C,
"PLASMA_COMPARTMENT",
pools={
Pool.ARTERIAL: "ARTERIAL_PLASMA",
Pool.VENOUS: "VENOUS_PLASMA_COMPARTMENT",
},
terms=_PLASMA,
),
"blood_cells": Kind(
_C,
"RED_BLOOD_CELL_COMPARTMENT",
terms=_BLOOD_CELLS,
),
"capacity": Kind(
SBO.IMPLICIT_COMPARTMENT,
"COMPARTMENT",
terms=(
(BQB.IS_VERSION_OF, pbpko("BLOOD_COMPARTMENT")),
),
requested="plasma-equivalent capacity of the blood (volume times BP)",
),
"organ": Kind(_C, "COMPARTMENT", is_place=True),
"tissue": Kind(
_C,
"COMPARTMENT",
terms=((BQB.IS, "uberon/UBERON:0000479"),),
requested="tissue compartment (interstitial and intracellular space)",
),
"interstitial": Kind(
_C,
"COMPARTMENT",
terms=(
(BQB.IS, "uberon/UBERON:0000913"),
(BQB.IS, "ncit/C120839"),
),
requested="interstitial compartment",
),
"intracellular": Kind(
_C,
"COMPARTMENT",
organ="{}_INTRACELLULAR_SPACE_COMPARTMENT",
terms=((BQB.IS, "go/GO:0005622"),),
requested="intracellular space compartment",
per_organ=False,
),
"urine": Kind(
_C,
"URINE_COMPARTMENT",
terms=tuple(_compartments["urine"]),
),
"feces": Kind(
_C,
"FECES_COMPARTMENT",
terms=tuple(_compartments["feces"]),
),
"bile": Kind(
_C,
"BILE_COMPARTMENT",
terms=tuple(_compartments["bi"]),
),
"lumen": Kind(
_C,
"GUT_LUMEN_COMPARTMENT",
terms=tuple(_compartments["gu_lumen"]),
),
"mucosa": Kind(
_C,
"COMPARTMENT",
terms=(
(BQB.IS, "uberon/UBERON:0001242"),
(
BQB.IS_PART_OF,
pbpko("INTESTINAL_TISSUE_COMPARTMENT"),
),
),
requested="intestinal mucosa compartment (enterocytes)",
),
"gut_wall": Kind(
_C,
"COMPARTMENT",
terms=(
(
BQB.IS_PART_OF,
pbpko("INTESTINAL_TISSUE_COMPARTMENT"),
),
),
requested="intestinal tissue compartment without the mucosa",
),
"tubule": Kind(_C, "FILTRATE_COMPARTMENT"),
"body_weight": Kind(_P, "BODYWEIGHT"),
"height": Kind(_P, "HEIGHT"),
"age": Kind(_P, "AGE_IN_PBPK_MODEL"),
"bmi": Kind(_P, "BODY_MASS_INDEX"),
"bsa": Kind(
_P,
"SURFACE_AREA",
terms=((BQB.IS, "ncit/C25157"),),
),
"lean_mass": Kind(
_P,
_PHYS,
terms=((BQB.IS, "ncit/C71258"),),
requested="fat-free mass",
),
"scaling_factor": Kind(
_P, _PHYS, requested="covariate scaling factor"
),
"organ_mass": Kind(
_P,
_PHYS,
organ="{}_MASS",
requested="mass of organ",
per_organ=False,
),
"organ_volume": Kind(
_P, "VOLUME_OF_COMPARTMENT", organ="VOLUME_OF_{}"
),
"blood_volume": Kind(_P, "VOLUME_OF_BLOOD"),
"pool_volume": Kind(
_P,
"VOLUME_OF_COMPARTMENT",
pools={
Pool.ARTERIAL: "ARTERIAL_VOLUME",
Pool.VENOUS: "VENOUS_VOLUME",
Pool.PORTAL: "VOLUME_OF_PORTAL_VEIN",
},
),
"pool_fraction": Kind(
_P,
_PHYS,
requested="fraction of the blood volume in a blood pool",
),
"vascular_fraction": Kind(
_P, "VOLUME_FRACTION_OF_BLOOD"
),
"interstitial_fraction": Kind(
_P,
_PHYS,
requested="interstitial volume fraction of an organ",
),
"tissue_volume": Kind(_P, "VOLUME_OF_COMPARTMENT"),
"zone_fraction": Kind(
_P,
_PHYS,
requested="volume fraction of a zone of the liver",
),
"hematocrit": Kind(
_P,
"VOLUME_FRACTION_OF_RED_BLOOD_CELLS",
terms=(
(BQB.IS_PROPERTY_OF, "uberon/UBERON:0000178"),
),
),
"cardiac_output": Kind(_P, "CARDIAC_OUTPUT_RATE"),
"flow_fraction": Kind(
_P,
"FRACTION_OF_BLOOD_FLOW_TO_A_COMPARTMENT",
organ="FRACTION_OF_BLOOD_FLOW_TO_{}",
),
"organ_flow": Kind(
_P,
"BLOOD_FLOW_RATE_TO_COMPARTMENT",
organ="BLOOD_FLOW_RATE_TO_{}",
),
"hepatic_artery_flow": Kind(
_P,
"BLOOD_FLOW_RATE_TO_COMPARTMENT",
requested="hepatic artery blood flow",
),
"portal_flow": Kind(
_P, "BLOOD_FLOW_RATE_TO_PORTAL_VEIN"
),
"hepatic_flow": Kind(_P, "HEPATIC_VEIN_BLOOD_FLOW"),
"gfr": Kind(_P, "GLOMERULAR_FILTRATION_RATE"),
"gfr_base": Kind(
_P,
_PHYS,
terms=(
(
BQB.IS_VERSION_OF,
pbpko("GLOMERULAR_FILTRATION_RATE"),
),
),
requested="glomerular filtration rate at normal renal function",
),
"egfr": Kind(
_P,
"GLOMERULAR_FILTRATION_RATE",
terms=((BQB.IS, "ncit/C110935"),),
),
"organ_function": Kind(
_P, _PHYS, requested="relative organ function"
),
"tubular_share": Kind(
_P,
_PHYS,
requested="share of the tubular capacity which follows the renal function",
),
"shunt": Kind(
_P, _PHYS, requested="portosystemic shunt fraction"
),
"child_pugh": Kind(
_P,
_PHYS,
terms=(_DISEASES["child_pugh"],),
requested="severity of hepatic impairment",
),
"heart_failure": Kind(
_P,
_PHYS,
terms=(_DISEASES["heart_failure"],),
requested="severity of heart failure",
),
"ckd": Kind(
_P,
_PHYS,
terms=(_DISEASES["ckd"],),
requested="stage of chronic kidney disease",
),
"cirrhosis_factor": Kind(
_P,
_PHYS,
terms=(_DISEASES["cirrhosis"],),
requested="impairment factor",
),
"ckd_factor": Kind(
_P,
_PHYS,
terms=(_DISEASES["ckd"],),
requested="impairment factor",
),
"heart_failure_factor": Kind(
_P,
_PHYS,
terms=(_DISEASES["heart_failure"],),
requested="impairment factor",
),
"impairment_factor": Kind(
_P, _PHYS, requested="impairment factor"
),
"molecular_weight": Kind(
SBO.MOLECULAR_MASS, "MOLECULAR_WEIGHT"
),
"fu": Kind(_P, "FRACTION_UNBOUND_PLASMA"),
"fraction_reabsorbed": Kind(_P, "RESORPTION"),
"reabsorption_threshold": Kind(
_P,
_BIOCHEM,
requested="renal threshold of a saturable reabsorption",
),
"reabsorption_n": Kind(
_P,
_BIOCHEM,
requested="sharpness of the renal threshold of a saturable reabsorption",
),
"baseline": Kind(
_P,
"CONCENTRATION_IN_PLASMA",
requested="endogenous baseline plasma concentration",
),
"steady_clearance": Kind(_P, "CLEARANCE_RATE"),
"steady_rate": Kind(
_P,
_BIOCHEM,
requested="net production rate at the steady state",
),
"steady_vmax": Kind(
SBO.MAXIMAL_VELOCITY, "MAXIMUM_RATE"
),
"steady_km": Kind(
SBO.MICHAELIS_CONSTANT,
_BIOCHEM,
requested="Michaelis constant",
),
"steady_plasma": Kind(_P, "CONCENTRATION_IN_PLASMA"),
"kp": Kind(_P, "TISSUE_PLASMA_PARTITION_COEFFICIENT"),
"kp_organ": Kind(
_P,
"TISSUE_PLASMA_PARTITION_COEFFICIENT",
organ="{}_PLASMA_PARTITION_COEFFICIENT",
),
"kp_factor": Kind(
_P,
_BIOCHEM,
requested="factor of the partition coefficients",
),
"partition": Kind(_P, "PARTITION_COEFFICIENT"),
"slow_pool_exchange": Kind(
_P,
_BIOCHEM,
requested="exchange rate constant of a slow tissue pool per tissue volume",
),
"tissue_composition": Kind(
_P,
_PHYS,
requested="tissue composition (water, protein, lipid fractions)",
),
"permeability": Kind(
_P,
_BIOCHEM,
requested="permeability surface area product (exchange flow)",
),
"bp": Kind(_P, "BLOOD_PLASMA_RATIO"),
"kbc": Kind(
_P, "RED_BLOOD_CELLS_PARTITION_COEFFICIENT"
),
"exchange_rate": Kind(
_P,
_BIOCHEM,
requested="exchange rate constant of plasma and blood cells",
),
"endothelial_exchange": Kind(
_P,
_PHYS,
requested="endothelial exchange rate constant per organ volume",
),
"activity": Kind(
SBO.RELATIVE_ACTIVITY,
_BIOCHEM,
requested="relative activity of enzyme or transporter",
),
"enzyme_amount": Kind(
SBO.RELATIVE_ACTIVITY,
_BIOCHEM,
requested="relative amount of enzyme or transporter",
),
"kdeg": Kind(
SBO.DECAY_CONSTANT, "DEGRADATION_RATE_CONSTANT"
),
"ki": Kind(
SBO.INHIBITORY_CONSTANT, "INHIBITION_CONSTANT"
),
"kinact": Kind(
SBO.INACTIVATION_RATE_CONSTANT,
_BIOCHEM,
requested="maximal inactivation rate constant",
),
"emax": Kind(
_P, _BIOCHEM, requested="maximal induction"
),
"ec50": Kind(
SBO.EC50,
_BIOCHEM,
requested="half-maximal effective concentration",
),
"placement_weight": Kind(
_P,
_MISC,
requested="abundance weight of a protein or process",
),
"vmax": Kind(
SBO.MAXIMAL_VELOCITY,
"MAXIMUM_RATE",
organ="MAXIMUM_RATE_IN_{}",
per_organ=False,
),
"vmax_basolateral": Kind(
SBO.MAXIMAL_VELOCITY,
"MAXIMUM_RATE_OF_BASOLATERAL_TRANSPORTER",
),
"vmax_apical": Kind(
SBO.MAXIMAL_VELOCITY,
"MAXIMUM_RATE_OF_APICAL_TRANSPORTER",
),
"km": Kind(
SBO.MICHAELIS_CONSTANT,
_BIOCHEM,
organ="MICHAELIS_CONSTANT__{}",
requested="Michaelis constant",
per_organ=False,
),
"km_basolateral": Kind(
SBO.MICHAELIS_CONSTANT, "MICHAELIS_CONSTANT_BASO"
),
"km_apical": Kind(
SBO.MICHAELIS_CONSTANT, "MICHAELIS_CONSTANT_APICAL"
),
"hill": Kind(SBO.HILL_COEFFICIENT, "HILL_COEFFICIENT"),
"k_metabolism": Kind(
SBO.KINETIC_CONSTANT, "INTRINSIC_CLEARANCE_RATE"
),
"k_influx": Kind(
SBO.KINETIC_CONSTANT, "CLEARANCE_RATE"
),
"k_efflux": Kind(
SBO.KINETIC_CONSTANT, "CLEARANCE_RATE"
),
"k_metabolism_volume": Kind(
SBO.KINETIC_CONSTANT,
_BIOCHEM,
terms=(
(
BQB.IS_VERSION_OF,
pbpko("INTRINSIC_CLEARANCE_RATE"),
),
),
requested="intrinsic clearance per organ volume",
),
"k_transport_volume": Kind(
SBO.KINETIC_CONSTANT,
_BIOCHEM,
terms=(
(BQB.IS_VERSION_OF, pbpko("CLEARANCE_RATE")),
),
requested="transport clearance per organ volume",
),
"rate_ratio": Kind(
_P,
_BIOCHEM,
requested="ratio of the capacity of a process to another process",
),
"product_fraction": Kind(
_P,
_BIOCHEM,
requested="fraction of a metabolism which forms a product",
),
"custom_parameter": Kind(None, _MISC),
"definition_parameter": Kind(None, _MISC),
"custom_species": Kind(
None, "CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT"
),
"custom_amount": Kind(
None, "AMOUNT_OF_COMPOUND_IN_COMPARTMENT"
),
"dose": Kind(
_P,
"PARAMETER",
terms=((BQB.IS, "ncit/C25488"),),
requested="dose",
),
"iv_time": Kind(
_P,
"PARAMETER",
terms=_IV_BOLUS,
requested="injection time of an intravenous dose",
),
"iv_rate": Kind(
SBO.FORWARD_RATE_CONSTANT,
"PARAMETER",
terms=_IV_BOLUS,
requested="injection rate constant of an intravenous dose",
),
"infusion_rate": Kind(
_P,
"PARAMETER",
terms=_IV_INFUSION,
requested="infusion rate of an intravenous infusion",
),
"dissolution": Kind(
_P, _MISC, requested="dissolution of a formulation"
),
"application_rate": Kind(
SBO.FORWARD_RATE_CONSTANT,
"ABSORPTION_RATE_CONSTANT",
),
"absorption_rate": Kind(
SBO.FORWARD_RATE_CONSTANT,
"ABSORPTION_RATE_CONSTANT_INTESTINE",
),
"transit_time": Kind(_P, "INTESTINAL_TRANSIT_TIME"),
"gastric_transit_time": Kind(
_P, _PHYS, requested="gastric emptying time"
),
"fed": Kind(
_P,
_MISC,
terms=((BQB.IS_VERSION_OF, "ncit/C65056"),),
requested="prandial state (fed or fasted)",
),
"intestine_geometry": Kind(
_P,
_PHYS,
requested="intestinal mucosa and absorption geometry",
),
"gut_flow": Kind(_P, "BLOOD_FLOW_RATE_TO_GUT"),
"gut_volume": Kind(_P, "VOLUME_OF_GUT"),
"mucosa_flow": Kind(
_P,
"BLOOD_FLOW_RATE_TO_COMPARTMENT",
requested="blood flow rate to intestinal mucosa",
),
"mucosa_volume": Kind(_P, "ENTEROCYTE_VOLUME"),
"bile_transit": Kind(
SBO.FORWARD_RATE_CONSTANT,
_PHYS,
requested="bile transit rate constant",
),
"tubule_fraction": Kind(
_P,
_PHYS,
requested="tubular flow fraction of the glomerular filtration rate",
),
"fraction_absorbed": Kind(
_P, "UPTAKE_FRACTION_TO_BLOOD"
),
"colon_absorption": Kind(
_P,
_PHYS,
requested="absorption factor of the large intestine",
),
"regional_absorption": Kind(
_P,
_BIOCHEM,
requested="relative absorption of a substance in an intestinal segment",
),
"lumen_conversion_rate": Kind(
SBO.FORWARD_RATE_CONSTANT,
_BIOCHEM,
requested="rate constant of a conversion in the intestinal lumen",
),
"arm_weight": Kind(
_P,
_PHYS,
requested="weight of a tissue in the arm vein sampling site",
),
"outflow": Kind(
_P,
"TOTAL_VENOUS_CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT",
),
"outflow_blood_cells": Kind(
_P, "CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT"
),
"organ_concentration": Kind(
_P, "CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT"
),
"organ_amount": Kind(
_P, "AMOUNT_OF_COMPOUND_IN_COMPARTMENT"
),
"plasma_concentration": Kind(
_P, "CONCENTRATION_IN_PLASMA"
),
"free_concentration": Kind(
_P, "UNBOUND_CONCENTRATION_IN_PLASMA"
),
"blood_concentration": Kind(
_P, "CONCENTRATION_IN_BLOOD"
),
"unbound_concentration": Kind(
_P,
"UNBOUND_CONCENTRATION_OF_COMPUND_IN_COMPARTMENT",
),
"urine_rate": Kind(
_P,
"OUTPUT_PARAMETER",
terms=((BQB.IS_VERSION_OF, pbpko("URINARY_RATE")),),
requested="urinary excretion rate (amount of compound per time)",
),
"lumen_amount": Kind(_P, "AMOUNT_IN_LUMEN"),
"intestine_absorption": Kind(
_P,
"OUTPUT_PARAMETER",
terms=((BQB.IS_VERSION_OF, pbpko("ABSORPTION")),),
requested="intestinal absorption rate (amount of compound per time)",
),
"intestine_efflux": Kind(
_P,
"OUTPUT_PARAMETER",
terms=(
(
BQB.IS_VERSION_OF,
pbpko("DISTRIBUTION_PROCESS"),
),
),
requested="intestinal efflux rate into the lumen (amount of compound per time)",
),
"feces_rate": Kind(
_P,
"OUTPUT_PARAMETER",
terms=(
(BQB.IS_VERSION_OF, pbpko("FECAL_EXCRETION")),
),
requested="fecal excretion rate (amount of compound per time)",
),
"absorbed_amount": Kind(
_P,
"OUTPUT_PARAMETER",
terms=((BQB.IS_VERSION_OF, pbpko("ABSORPTION")),),
requested="amount of compound absorbed from the intestinal lumen",
),
"absorbed_fraction": Kind(
_P,
"OUTPUT_PARAMETER",
terms=((BQB.IS_VERSION_OF, pbpko("ABSORPTION")),),
requested="fraction of the oral dose absorbed from the intestinal lumen",
),
"oral_dose_applied": Kind(
_P,
"OUTPUT_PARAMETER",
requested="amount of the oral dose applied to the intestinal lumen",
),
"observer": Kind(_P, "OUTPUT_PARAMETER"),
"concentration": Kind(
_SPECIES, "CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT"
),
"concentration_plasma": Kind(
_SPECIES, "CONCENTRATION_IN_PLASMA"
),
"concentration_tissue": Kind(
_SPECIES,
"CONCENTRATION_OF_COMPOUND_IN_COMPARTMENT",
organ="CONCENTRATION_IN_{}",
),
"concentration_lumen": Kind(
_SPECIES, "CONCENTRATION_IN_LUMEN"
),
"concentration_mucosa": Kind(
_SPECIES, "CONCENTRATION_IN_INTESTINAL_TISSUE"
),
"concentration_bile": Kind(
_SPECIES, "CONCENTRATION_IN_BILE"
),
"concentration_tubule": Kind(
_SPECIES, "CONCENTRATION_IN_FILTRATE"
),
"amount_urine": Kind(
_SPECIES, "CUMULATIVE_AMOUNT_IN_URINE"
),
"amount_feces": Kind(
_SPECIES, "CUMULATIVE_AMOUNT_IN_FECES"
),
"amount_undissolved": Kind(
_SPECIES,
"AMOUNT_IN_LUMEN",
requested="amount of undissolved drug",
),
"blood_flow": Kind(
_T,
"DISTRIBUTION_PROCESS",
terms=((BQB.IS, "go/GO:0008015"),),
),
"exchange": Kind(_T, "DISTRIBUTION_PROCESS"),
"metabolism": Kind(
SBO.BIOCHEMICAL_REACTION,
"LINEAR_ELIMINATION",
terms=((BQB.IS, "go/GO:0008152"),),
),
"metabolism_saturable": Kind(
SBO.BIOCHEMICAL_REACTION,
"NON_LINEAR_ELIMINATION",
terms=((BQB.IS, "go/GO:0008152"),),
),
"gut_metabolism": Kind(
SBO.BIOCHEMICAL_REACTION,
"GUT_METABOLISM",
terms=((BQB.IS, "go/GO:0008152"),),
),
"metabolism_product": Kind(
SBO.BIOCHEMICAL_REACTION,
None,
terms=((BQB.IS_PART_OF, "go/GO:0008152"),),
),
"transport": Kind(
_T,
"DISTRIBUTION_PROCESS",
terms=((BQB.IS, "go/GO:0055085"),),
),
"biliary_excretion": Kind(
_T,
"BILIARY_ELIMINATION",
terms=((BQB.IS, "go/GO:0055085"),),
),
"renal_secretion": Kind(
_T,
"RENAL_EXCRETION",
terms=((BQB.IS, "go/GO:0097254"),),
),
"reabsorption": Kind(
_T,
"RESORPTION",
terms=((BQB.IS, "go/GO:0055085"),),
),
"filtration": Kind(
_T,
"RENAL_EXCRETION",
terms=((BQB.IS, "go/GO:0003094"),),
),
"tubular_flow": Kind(
_T,
None,
terms=(
(BQB.IS_PART_OF, pbpko("RENAL_EXCRETION")),
(BQB.IS_PART_OF, "go/GO:0007588"),
),
),
"absorption": Kind(
_T,
"ABSORPTION",
terms=((BQB.IS, "go/GO:0050892"),),
),
"dissolution_reaction": Kind(
_T,
None,
terms=((BQB.IS_PART_OF, pbpko("ABSORPTION")),),
requested="dissolution process",
),
"transit": Kind(
_T,
None,
terms=((BQB.IS_VERSION_OF, "go/GO:0022600"),),
requested="gastrointestinal transit process",
),
"fecal_excretion": Kind(
_T,
"FECAL_EXCRETION",
terms=((BQB.IS, "go/GO:0007588"),),
),
"lumen_conversion": Kind(
SBO.BIOCHEMICAL_REACTION,
None,
terms=(
(BQB.IS_VERSION_OF, pbpko("GUT_METABOLISM")),
),
requested="conversion in the intestinal lumen",
),
"bile_flow": Kind(
_T,
None,
terms=(
(
BQB.IS_PART_OF,
pbpko("ENTEROHEPATIC_RECIRCULATION"),
),
),
),
"iv_application": Kind(
_T,
None,
terms=(
(
BQB.IS_VERSION_OF,
pbpko("INTRAVENOUS_BOLUS_EXPOSURE"),
),
(
BQB.IS_VERSION_OF,
pbpko("INTRAVENOUS_INFUSION_EXPOSURE"),
),
),
),
"oral_application": Kind(_T, "ORAL_EXPOSURE"),
"custom_reaction": Kind(
SBO.BIOCHEMICAL_OR_TRANSPORT_REACTION,
None,
terms=((BQB.IS_VERSION_OF, "go/GO:0008150"),),
),
}
The kinds of the elements the library creates.
dataclass
¶
Kind(
sbo,
pbpko,
organ=None,
pools=dict(),
terms=(),
requested=None,
per_organ=True,
is_place=False,
)
What an element is: its SBO term and its ontology terms.
Attributes:
| Name | Type | Description |
|---|---|---|
sbo |
str | None
|
the SBO term, |
pbpko |
str | None
|
the name of the PBPKO term, the broader term where PBPKO has
no term for the kind ( |
organ |
str | None
|
the name of the organ-specific PBPKO term with |
pools |
Mapping[Pool, str]
|
the PBPKO term of the kind by blood pool, which replaces
|
terms |
tuple[Term, ...]
|
further terms of the kind ( |
requested |
str | None
|
the PBPKO term which is missing, if |
per_organ |
bool
|
the organ-specific terms which PBPKO lacks are requested
for every organ (the physiology), not only where PBPKO has some
(the kinetics of the processes, |
is_place |
bool
|
the element is the place itself (the whole organ of a
flow-limited organ), so the terms of the place are |
Get the resource of a term of the pinned PBPKO by its name.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
the name of the term in the pymetadata enum, |
required |
Returns:
| Type | Description |
|---|---|
str
|
The resource |
str
|
does not register PBPKO, so pymetadata cannot parse a |
str
|
|
str
|
identifiers.org url which does not resolve); the bioregistry url is |
str
|
written as given and resolves. |
Raises:
| Type | Description |
|---|---|
AttributeError
|
if PBPKO has no term of the name. |
Get the initial assignment of a constant, with a name and an SBO term.
Every quantity of the library which depends on parameters only is a constant with an initial assignment; the assignment carries the name of its target and the SBO term of a mathematical expression, so the factory has nothing to hint about.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
symbol
|
str
|
the id of the target. |
required |
formula
|
str
|
the formula. |
required |
unit
|
UnitType
|
the unit of the formula. |
required |
name
|
str
|
the name of the target. |
required |
Returns:
| Type | Description |
|---|---|
InitialAssignment
|
The initial assignment. |
annotate(
element,
kind,
*,
organ=None,
pool=None,
segment=None,
site=None,
protein=None,
substance=None,
)
Annotate an element the library creates by its kind and its place.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
element
|
S
|
the compartment, species, parameter or reaction. |
required |
kind
|
str
|
the kind of the element, a key of |
required |
organ
|
Organ | None
|
the organ of the element. |
None
|
pool
|
Pool | None
|
the blood pool of the element. |
None
|
segment
|
str | None
|
the lumen segment of the element ( |
None
|
site
|
str | None
|
the sampling site of an observer, a key of |
None
|
protein
|
str | None
|
the protein of a process or of its parameters; a protein
which is not in the protein table adds no terms (a definition
checks its proteins, |
None
|
substance
|
Substance | None
|
the substance of a species, whose annotations it takes. |
None
|
Returns:
| Type | Description |
|---|---|
S
|
The element, with the SBO term of the kind (a kind which keeps the |
S
|
SBO term of the element gives a generic one to an element without) |
S
|
and its terms added to its annotations; a term of the place whose |
S
|
resource the element has already (as what it is) is not repeated. |
Raises:
| Type | Description |
|---|---|
KeyError
|
if the kind, the segment or the site is unknown. |
Get the annotations of a PBPK model: its type, the taxon and the approach.
A model is perfusion-limited when every substance which enters tissue
does so flow-limited (Mode.PERFUSION), permeability-limited when one
has a finite exchange.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
substances
|
Iterable[Substance]
|
the substances of the model. |
required |
Returns:
| Type | Description |
|---|---|
list[Term]
|
The terms of the model. |
Get the PBPKO terms the library needs and the pinned PBPKO lacks.
Returns:
| Name | Type | Description |
|---|---|---|
dict[str, str]
|
The missing terms with the broader PBPKO term the library uses |
|
instead |
dict[str, str]
|
the |
dict[str, str]
|
terms of the kinds which PBPKO lacks for an organ. |
values¶
Values with provenance.
A number of a PBPK model is a Value: the number, its unit and where it
comes from (a key of data/sources.toml, see pkpdsim.pbpk.data). A fitted
value is a Value as well, from the keyword arguments of a fit record. A
value which is tied to other parameters (a metabolite with the Kp of its
parent, a fixed ratio) is a Formula over ids of the top model, written as
the initial assignment of its parameter. A constant which no field of the
library holds is a ModelParameter with such a value.
module-attribute
¶
An SBML SId, the ids of a definition (substances, processes, parameters).
dataclass
¶
A number with unit and provenance.
Attributes:
| Name | Type | Description |
|---|---|---|
value |
float
|
the number. |
unit |
UnitType
|
the unit of the number. |
source |
str | None
|
the key of the source in |
notes |
str | None
|
a remark on the value. |
uncertainties |
list[Uncertainty] | None
|
the uncertainty of a fitted value. |
dataclass
¶
A value tied to other parameters: a formula over ids of the top model.
The parameter of the value gets the formula as its initial assignment, as
the covariates do: a change of a parameter it reads before the
simulation is followed, and an id of PBPKDefinition.dynamic keeps it an
assignment rule. The ids of the formula are constant parameters and
compartments of the top model (the parameters of the substances, the
covariates, the physiology), also for a value of an organ, which reads
them through input ports under the same ids; the build refuses an id the
top model does not have and the species and observers (they change during
the simulation). The unit is the unit of the parameter, it is not inferred
from the formula.
One exception reads the ids of an organ instead: the steady state of a
custom reaction (CustomReaction.stationary) is a Formula of the
organ, as its rate law, over the elements of the organ (Vti, the
parameters of the reaction, species of other substances at their start)
and constants of the top model; the Formula of a ModelParameter of a
custom reaction reads the constants of its organ which are no ids of the
top model as well (another parameter of a custom reaction of the organ,
Vti); every other Formula (a value, a parameter of the definition, a
start of PBPKDefinition.starts, a baseline) reads the ids of the top
model only.
Attributes:
| Name | Type | Description |
|---|---|---|
expression |
str
|
the formula (SBML L3 infix), e.g. |
unit |
UnitType
|
the unit of the parameter. |
notes |
str | None
|
a remark on the value, e.g. why it is tied. |
dataclass
¶
A constant parameter which the model package states, with its provenance.
In PBPKDefinition.parameters a constant of the top model which no field
of the library holds (a production rate which the baseline of a
substance and a custom reaction of the muscle share): the formulas of the
definition, its observers and the custom reactions of the organs read it
under its id, an organ through an input port under the same id. In
CustomReaction.parameters a constant of the organ of the reaction (a
fitted constant of the mechanism): a local id of the organ, which the
reactions of the organ read, <ORGAN>__<id> in the flat model.
Attributes:
| Name | Type | Description |
|---|---|---|
sid |
str
|
the id of the parameter, an id of the top model which is no id of the library, or a local id of the organ. |
value |
Q
|
the number in |
unit |
UnitDefinition
|
the unit of the parameter. |
name |
str | None
|
the name of the parameter, the id by default. |
notes |
str | None
|
the notes of the parameter, e.g. its meaning and source. |
Bases: Mapping[str, V]
A read-only, hashable mapping from an id to a value.
The mapping fields of the frozen dataclasses of a definition (the values
per substance of the intestine, PerSubstance; the starts of the
species, PBPKDefinition.starts; the regional absorption profiles per
substance, whose values are profiles) are kept as this copy: it reads back as
a Mapping (ka["a"], .items()), cannot be changed after the
validation and is hashed by its items (a dict is unhashable).
Copy the items.
Get the value of a fitted parameter.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
kwargs
|
Mapping[str, Any]
|
the keyword arguments of |
required |
source
|
str
|
the provenance of the value. |
'fit'
|
notes
|
str | None
|
a remark on the value, e.g. the literature of the process; the provenance of the fit is in the uncertainties. |
None
|
Returns:
| Type | Description |
|---|---|
Value
|
The value with the uncertainty of the fit. |
Compare two parts of a definition by their values.
The objects of sbmlutils which a definition holds (the Uncertainty of a
fitted value, a Parameter or Species of a custom reaction) have no
equality of their own and compare by identity, so two definitions which
take the same fitted value from a fit record (fitted(FITS.parameter(...))
creates new uncertainties at every call) would differ. Here a dataclass
is equal by its equality (PDComponent by the id of its model, its
inputs and outputs) or by its fields, a mapping by its items, a list or
tuple by its elements, and an object which compares by identity by the
fields of its __dict__, each by value; every other object (numbers,
strings, enum members, a Creator) by ==.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
a
|
object
|
the one object. |
required |
b
|
object
|
the other object. |
required |
Returns:
| Type | Description |
|---|---|
bool
|
Whether they are equal by value. |
Check that a Value is given in the unit of its parameter.
The numbers of a definition are in the units of the model; a Value in
another unit (an exchange in l/min where one per litre of organ is meant)
would be taken as it is.
The definition of a unit, e.g. 1/min, the id of a unit of a kind (dimensionless).
Check the fields of a dataclass which are typed with a Literal.
A definition written in a script or a notebook may give any text: a text which is none of the choices would select no branch of the builder (a route without doses, an erythrocyte mode treated as another), so it raises.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
obj
|
object
|
the dataclass instance. |
required |
Raises:
| Type | Description |
|---|---|
ValueError
|
if a field holds none of its choices, naming the field and the allowed values. |
data¶
The data files of the PBPK library.
The data are TOML files in pkpdsim/pbpk/data. A number is a table
{ value = 1.8, unit = "kg", source = "ICRP89" } whose source is a key of
sources.toml, so every number states where it comes from.
dataclass
¶
A publication a number is taken from.
Attributes:
| Name | Type | Description |
|---|---|---|
key |
str
|
the key of the source, e.g. |
citation |
str
|
the citation. |
doi |
str | None
|
the DOI of the publication. |
Load a data file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
the name of the file without extension, e.g. |
required |
Returns:
| Type | Description |
|---|---|
dict[str, Any]
|
The content of |
Get a number of a data file with its unit, source and notes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
the name of the file without extension, e.g. |
required |
section
|
str
|
the table of the number. |
required |
key
|
str
|
the key of the number in the table. |
required |
Returns:
| Type | Description |
|---|---|
Value
|
The value. |
Raises:
| Type | Description |
|---|---|
ValueError
|
if the unit of the number is not a unit of the model. |
Get the citation of a source with its DOI.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
key
|
str
|
the key of the source. |
required |
Returns:
| Type | Description |
|---|---|
str
|
The citation, followed by the DOI if the source has one. |
Raises:
| Type | Description |
|---|---|
KeyError
|
if no source has the key. |
units¶
The units of the PBPK models.
Time is in min, substance in mmole, volume in litre and area in m2, the
model_units of the models. Every unit of U is a unit definition of every
model; a unit outside U (EXTRA_UNITS, ML_PER_MIN_1P73M2) is one only of
a model which uses it.
module-attribute
¶
ML_PER_MIN_1P73M2 = UnitDefinition(
"ml_per_min_1p73m2",
"ml/min/(1.73*meter^2)",
name="ml/min/1.73 m2",
)
Millilitre per minute per 1.73 m2 body surface area, the unit of a clearance or a
GFR per body surface area (eGFR, CLrenal/BSA).
1 ml/min/1.73 m2 = 1e-3/1.73 l/min/m2: a quantity in l/min divided by the
body surface area BSA (m2) is 1730 times the number in this unit, in
consistent units GFR / BSA * 1730 ml_per_min_1p73m2 * 1 m2 / 1 l_per_min.
Not a unit of U, so the models without it keep their unit definitions; a
model defines it wherever it uses it (an observer, a parameter of the
definition, a custom reaction, a number of a formula).
module-attribute
¶
EXTRA_UNITS = (ML_PER_MIN_1P73M2,)
The units of the library outside U: a model defines one when it uses it, as
the unit of an element or by its id in a formula.
module-attribute
¶
The text of a unit of EXTRA_UNITS on a figure, by the unit id.
sbmlsim writes a unit which pint does not read (a unit id of the model,
ml_per_min_1p73m2) on an axis as it is given; the figures show this text
instead (unit_label, axis). The words of a text are joined by a
non-breaking space (U+00A0, 1.73 m²): sbmlsim wraps a label which is longer
than its axis at its spaces, and a unit is not broken. The unit definition
keeps its name in the SBML.
Bases: Units
UnitDefinitions.
The text of a unit on a figure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
unit
|
str | None
|
the unit of an axis, a unit id of the model or a unit which pint reads. |
required |
Returns:
| Type | Description |
|---|---|
str
|
The text of |
str
|
short form of sbmlsim ( |
An axis of sbmlsim in a unit, with the text of the unit on the figure.
The unit stays what the data and the model are converted to
(ml_per_min_1p73m2, a unit of the model), the label of the axis is
<label> [<unit_label(unit)>]: a clearance per body surface area reads
[ml/min/1.73 m²], not the unit id which sbmlsim writes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
label
|
str
|
the label of the axis. |
required |
unit
|
str | None
|
the unit of the axis. |
required |
**kwargs
|
Any
|
further arguments of |
{}
|
Returns:
| Type | Description |
|---|---|
Axis
|
The axis, its |