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PBPK Ontology (PBPKO)

The PBPK (Physiologically-Based Pharmacokinetic) ontology is designed to support the modeling and understanding of pharmacokinetics in biological systems. This documentation provides an overview of the ontology development workflow, the imported ontologies, and the specific terms used in PBPK ontology.

Detailed Documentation

Detailed documentation of ontology can be found at this link

Development Workflow

The development of the PBPK ontology leverages the ROBOT (ROBOT is an OBO Tool) framework, which provides powerful tools for ontology development, including ontology merging, reasoning, and template-based term generation.

Ontology Imports

The PBPKO ontology imports several foundational ontologies to ensure interoperability and adherence to ontological best practices:

  1. Basic Formal Ontology (BFO)
  2. Relation Ontology (RO)
  3. Gene Ontology (GO)
  4. Ontology for Biomedical Investigations (OBI)
  5. Systems Biology Ontology

Integration with BFO

graph TB %% Legend subgraph Legend direction TB class_legend((Class)) subclass_legend-.->class_legend property_legend((Object Property)) property_legend--"Object Property"-->class_legend end %% Ontology Imports (BFO, OBI, GO, SBO) subgraph Imported_Ontologies["Imported Ontologies"] direction LR subgraph BFO["BFO"] direction TB BFO_0000002((BFO:entity)) BFO_0000020((BFO:continuant)) BFO_0000051---BFO_0000020("has_part") BFO_specifically_dependent((BFO:specifically dependent continuant)) BFO_occurrent((BFO:occurrent)) BFO_process((BFO:process)) end subgraph OBI["OBI"] direction TB OBI_0000658((OBI:data representation model)) end subgraph GO["GO"] direction TB GO_0008150((GO:biological process)) GO_0007588((GO:excretion)) GO_0008150---GO_0007588 end subgraph SBO["SBO"] direction TB SBO_0000027((SBO:Michaelis constant)) end %% Links between imported ontologies BFO_0000002---BFO_0000020 BFO_0000020---BFO_specifically_dependent BFO_0000002---BFO_occurrent BFO_occurrent---BFO_process BFO_process---GO_0008150 BFO_specifically_dependent---OBI_0000658 end %% PBPKO Main Classes subgraph PBPKO["PBPK Ontology (PBPKO)"] direction TB subgraph Core_Components direction TB PBPKO_00003((PBPKO:physiologically based pharmacokinetic model)) PBPKO_00446((PBPKO:compartment)) PBPKO_00217((PBPKO:transporter)) %% PBPKO_enzyme - derived from definitions/context PBPKO_enzyme((PBPKO:enzyme)) end subgraph Biological_Processes direction TB PBPKO_00140((PBPKO:absorption)) PBPKO_00146((PBPKO:distribution)) %% Corrected parent based on definition PBPKO_00322((PBPKO:elimination)) PBPKO_00188((PBPKO:metabolism)) PBPKO_00238((PBPKO:biliary elimination)) end subgraph Parameters direction TB PBPKO_00002((PBPKO:parameter)) PBPKO_00006((PBPKO:physiological parameter)) PBPKO_00126((PBPKO:physicochemical parameter)) PBPKO_00139((PBPKO:biochemical parameter)) PBPKO_00239((PBPKO:route of exposure)) PBPKO_00252((PBPKO:output parameter)) end %% PBPKO Hierarchy OBI_0000658---PBPKO_00003 OBI_0000658---PBPKO_00446 BFO_0000002---PBPKO_00217 BFO_0000002---PBPKO_enzyme GO_0008150---PBPKO_00140 GO_0008150---PBPKO_00146 GO_0008150---PBPKO_00322 GO_0008150---PBPKO_00188 PBPKO_00322---GO_0007588 PBPKO_00322---PBPKO_00238 BFO_specifically_dependent---PBPKO_00002 PBPKO_00002---PBPKO_00006 PBPKO_00002---PBPKO_00126 PBPKO_00002---PBPKO_00139 PBPKO_00002---PBPKO_00239 PBPKO_00002---PBPKO_00252 PBPKO_00139---SBO_0000027 %% Example Subclasses PBPKO_00006---PBPKO_vol((PBPKO:volume of compartment)) PBPKO_00006---PBPKO_bf((PBPKO:blood flow to compartment)) PBPKO_00139---PBPKO_pc((PBPKO:partition coefficient)) PBPKO_00139---PBPKO_uf((PBPKO:unbound fraction)) PBPKO_00126---PBPKO_mw((PBPKO:molecular weight)) PBPKO_00446---PBPKO_central((PBPKO:central compartment)) PBPKO_00446---PBPKO_peripheral((PBPKO:peripheral compartment)) PBPKO_00446---PBPKO_liver_cpt((PBPKO:liver compartment)) PBPKO_00446---PBPKO_kidney_cpt((PBPKO:kidney compartment)) PBPKO_00252---PBPKO_conc_cpt((PBPKO:concentration of compound in compartment)) PBPKO_00252---PBPKO_amount_cpt((PBPKO:amount of compound in compartment)) PBPKO_00252---PBPKO_peak_conc((PBPKO:peak concentration)) PBPKO_00252---PBPKO_auc((PBPKO:area under curve)) end %% PBPKO Object Properties PBPKO_00003--"has_biological_process (PBPKO_10001)"-->PBPKO_00140 PBPKO_00003--"has_biological_process (PBPKO_10001)"-->PBPKO_00146 PBPKO_00003--"has_biological_process (PBPKO_10001)"-->PBPKO_00322 PBPKO_00003--"has_biological_process (PBPKO_10001)"-->PBPKO_00188 PBPKO_00003--"has_compartment (PBPKO_10002)"-->PBPKO_00446 PBPKO_00003--"has_transporter (PBPKO_10004)"-->PBPKO_00217 %% Using the general has_parameter property PBPKO_00003--"has_parameter (PBPKO_10005)"-->PBPKO_00006 PBPKO_00003--"has_parameter (PBPKO_10005)"-->PBPKO_00126 PBPKO_00003--"has_parameter (PBPKO_10005)"-->PBPKO_00139 PBPKO_00003--"has_parameter (PBPKO_10005)"-->PBPKO_00239 PBPKO_00003--"has_parameter (PBPKO_10005)"-->PBPKO_00252 %% Example of object property subclass PBPKO_10005---PBPKO_10008((PBPKO:has_physiological_parameter)) PBPKO_10008--"has_physiological_parameter"-->PBPKO_00006 %% Link object properties to their domain BFO_0000051((BFO:has_part)) %% Link PBPKO properties to their superproperty BFO_0000051---PBPKO_10001 BFO_0000051---PBPKO_10002 BFO_0000051---PBPKO_10004 BFO_0000051---PBPKO_10005

PBPK Terms Vocabulary

PBPK terms are available in ROBOT template

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