Remove redundant volume parameters

README.md

@@ -26,8 +26,6 @@ The converted SBML file does not yet contain annotations of terms and units. It
 
 An initial version of an annotations file is available (see, [euromix.annotations.csv](model/euromix.annotations.csv)). This demonstrates how elements of the model are related to ontology terms and units. The script [annotate_sbml_terms.py](src/python/annotate_sbml.py) combines the model file and annotations file to obtain an SBML file with annotated terms. The script [annotate_sbml_units.py](src/python/annotate_sbml_units.py) combines the model file and annotations file to obtain an SBML file with annotated units. Both scripts are heavily inspired by the [sbmlUtils](https://github.com/matthiaskoenig/sbmlutils) package. What remains to be done is to establish the vocabularies/ontologies to use for annotation and decide on the annotation requirements. I.e., what needs to be annotated? Also, it remains unclear how to distinguish different substances from species (in case of multiple-substance models).
 
-Notebook [test_model_annotation.ipynb](notebooks/test_model_annotation.ipynb) shows how to annotate the model using an annotations file.
-
 ## SBML validation [in progress]
 
 Automatic validation can be included to check for model errors, model consistency, consitency of units, and also on more PBK-model specific aspects (such as mass balance). The script [validate_sbml.py](src/python/validate_sbml.py) can be run to run validation checks on the SBML file. This is a first version in which some rudimentary file and consistency checks are performed. This first version is inspired by the [example](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/validate_s_b_m_l_8py-example.html) presented in the libSBML documentation.

model/euromix.ant

@@ -69,20 +69,9 @@ model euromix()
   ## Physiology
 
   ### Body size
-  const VFat := BM * scVFat / rho
-  const VRich := BM * scVRich / rho
-  const VLiver := BM * scVLiver / rho
-  const VBlood := BM * scVBlood / rho
-  const VArt := VBlood / 3.0
-  const VVen := VBlood - VArt
-  const VSkin_e := BSA * Height_vs * fSA_exposed
-  const VSkin_u := BSA * Height_vs * (1 - fSA_exposed)
-  const VSkin_sc_e := BSA * Height_sc * fSA_exposed
-  const VSkin_sc_u := BSA * Height_sc * (1 - fSA_exposed)
-  const VPoor := (BM / rho) - VFat - VRich - VLiver - VSkin_e - VSkin_u - VSkin_sc_e - VSkin_sc_u - VBlood - 0.1 * (BM / rho)
-
   const f_su := Kp_sc_vs * BSA * (1 - fSA_exposed)
   const f_se := Kp_sc_vs * BSA * fSA_exposed
+  const VBlood := BM * scVBlood / rho
 
   ### Flow rates
   const FBlood := scFBlood * BM
@@ -95,17 +84,17 @@ model euromix()
   const FSkin_u := FSkin - FSkin_e
 
   # Compartments and Species
-  compartment Fat := VFat
-  compartment Rich := VRich
-  compartment Poor := VPoor
-  compartment Liver := VLiver
+  compartment Fat := BM * scVFat / rho
+  compartment Rich := BM * scVRich / rho
+  compartment Liver := BM * scVLiver / rho
+  compartment Art := VBlood / 3.0
+  compartment Ven := VBlood - Art
+  compartment Skin_e := BSA * Height_vs * fSA_exposed
+  compartment Skin_u := BSA * Height_vs * (1 - fSA_exposed)
+  compartment Skin_sc_e := BSA * Height_sc * fSA_exposed
+  compartment Skin_sc_u := BSA * Height_sc * (1 - fSA_exposed)
+  compartment Poor := (BM / rho) - Fat - Rich - Liver - Skin_e - Skin_u - Skin_sc_e - Skin_sc_u - VBlood - 0.1 * (BM / rho)
   compartment Gut
-  compartment Skin_u := VSkin_u
-  compartment Skin_e := VSkin_e
-  compartment Skin_sc_u := VSkin_sc_u
-  compartment Skin_sc_e := VSkin_sc_e
-  compartment Art := VArt
-  compartment Ven := VVen
 
   # Species
   substanceOnly species QFat in Fat

model/euromix.terms.csv

@@ -66,15 +66,5 @@ scVRich,parameter,scVRich,richly perfused tissues (viscera) as fraction of total
 scVLiver,parameter,scVLiver,liver as fraction of total body volume,rdf,BQB_IS,uo/UO:0000193,fraction,
 scVBlood,parameter,scVBlood,blood as fraction of total body volume,rdf,BQB_IS,uo/UO:0000194,fraction,
 Vmax,parameter,Vmax,maximum rate of metabolism,rdf,BQB_IS,sbo/SBO:0000186,maximal velocity,Using generic term for maximal velocity.
-VFat,parameter,VFat,volume of adipose tissue,rdf,BQB_IS,pato/PATO:0000918,volume,
-VArt,parameter,VArt,arterial blood volume,rdf,BQB_IS,pato/PATO:0000918,volume,
 VBlood,parameter,VBlood,total blood volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VLiver,parameter,VLiver,liver volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VPoor,parameter,VPoor,poorly perfused tissue volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VVen,parameter,VVen,venous blood volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VRich,parameter,VRich,richly perfused tissue volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VSkin_e,parameter,VSkin_e,exposed skin volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VSkin_u,parameter,VSkin_u,unexposed skin volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VSkin_sc_e,parameter,VSkin_sc_e,stratum corneum exposed skin volume,rdf,BQB_IS,pato/PATO:0000918,volume,
-VSkin_sc_u,parameter,VSkin_sc_u,stratum corneum unexposed skin volume,rdf,BQB_IS,pato/PATO:0000918,volume,
 rho,parameter,rho,density of the tissues,rdf,BQB_IS,http://purl.obolibrary.org/obo/NCIT_C45781,density,

model/euromix.units.csv

@@ -1,4 +1,4 @@
-element_id,sbml_type,unit
+element_id,sbml_type,unit
 timeUnits,document,s
 substanceUnits,document,mmol
 volumeUnits,document,L
@@ -36,20 +36,8 @@ scVFat,parameter,unitless
 scVRich,parameter,unitless
 scVLiver,parameter,unitless
 scVBlood,parameter,unitless
-VFat,parameter,L
-VFat,parameter,L
-VFat,parameter,L
-VRich,parameter,L
-VLiver,parameter,L
 VBlood,parameter,L
-VArt,parameter,L
-VVen,parameter,L
-VSkin_e,parameter,L
 fSA_exposed,parameter,unitless
-VSkin_u,parameter,L
-VSkin_sc_e,parameter,L
-VSkin_sc_u,parameter,L
-VPoor,parameter,L
 rho,parameter,kg/L
 scFBlood,parameter,L.kg-1.h-1
 scFFat,parameter,unitless

notebooks/euromix.annotations.csv

@@ -2,15 +2,15 @@ id,sbml_type,name,unit,pattern,annotation_type,qualifier,resource
 default_compartment,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",default_compartment,rdf,BQB_IS,
 Fat,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Fat,rdf,BQB_IS,
 Rich,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Rich,rdf,BQB_IS,
-Poor,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Poor,rdf,BQB_IS,
 Liver,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Liver,rdf,BQB_IS,
-Gut,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Gut,rdf,BQB_IS,
-Skin_u,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_u,rdf,BQB_IS,
-Skin_e,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_e,rdf,BQB_IS,
-Skin_sc_u,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_sc_u,rdf,BQB_IS,
-Skin_sc_e,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_sc_e,rdf,BQB_IS,
 Art,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Art,rdf,BQB_IS,
 Ven,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Ven,rdf,BQB_IS,
+Skin_e,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_e,rdf,BQB_IS,
+Skin_u,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_u,rdf,BQB_IS,
+Skin_sc_e,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_sc_e,rdf,BQB_IS,
+Skin_sc_u,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Skin_sc_u,rdf,BQB_IS,
+Poor,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Poor,rdf,BQB_IS,
+Gut,compartment,,"litre (exponent = 1, multiplier = 1, scale = 0)",Gut,rdf,BQB_IS,
 QFat,species,,"mole (exponent = 1, multiplier = 1, scale = -3)",QFat,rdf,BQB_IS,
 QRich,species,,"mole (exponent = 1, multiplier = 1, scale = -3)",QRich,rdf,BQB_IS,
 QPoor,species,,"mole (exponent = 1, multiplier = 1, scale = -3)",QPoor,rdf,BQB_IS,
@@ -39,6 +39,7 @@ scFPoor,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",scF
 scFLiver,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",scFLiver,rdf,BQB_IS,
 scFSkin,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",scFSkin,rdf,BQB_IS,
 Falv,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",Falv,rdf,BQB_IS,
+rho,parameter,,"gram (exponent = 1, multiplier = 1, scale = 3), litre (exponent = -1, multiplier = 1, scale = 0)",rho,rdf,BQB_IS,
 PCFat,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",PCFat,rdf,BQB_IS,
 PCLiver,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",PCLiver,rdf,BQB_IS,
 PCRich,parameter,,"dimensionless (exponent = 1, multiplier = 1, scale = 0)",PCRich,rdf,BQB_IS,
@@ -55,19 +56,9 @@ Kp_sc_vs,parameter,,"metre (exponent = 1, multiplier = 1, scale = -1), second (e
 kGut,parameter,,"second (exponent = -1, multiplier = 3600, scale = 1)",kGut,rdf,BQB_IS,
 CLH,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",CLH,rdf,BQB_IS,
 Ke,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",Ke,rdf,BQB_IS,
-VFat,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VFat,rdf,BQB_IS,
-VRich,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VRich,rdf,BQB_IS,
-VLiver,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VLiver,rdf,BQB_IS,
+f_su,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",f_su,rdf,BQB_IS,
+f_se,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",f_se,rdf,BQB_IS,
 VBlood,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VBlood,rdf,BQB_IS,
-VArt,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VArt,rdf,BQB_IS,
-VVen,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VVen,rdf,BQB_IS,
-VSkin_e,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VSkin_e,rdf,BQB_IS,
-VSkin_u,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VSkin_u,rdf,BQB_IS,
-VSkin_sc_e,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VSkin_sc_e,rdf,BQB_IS,
-VSkin_sc_u,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VSkin_sc_u,rdf,BQB_IS,
-VPoor,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0)",VPoor,rdf,BQB_IS,
-f_su,parameter,,indeterminable,f_su,rdf,BQB_IS,
-f_se,parameter,,indeterminable,f_se,rdf,BQB_IS,
 FBlood,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",FBlood,rdf,BQB_IS,
 FFat,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",FFat,rdf,BQB_IS,
 FPoor,parameter,,"litre (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 3600, scale = 1)",FPoor,rdf,BQB_IS,