Ontology of Physics for Biology BFO and OBO

Ontology of Physics for Biology — BFO and OBO compliant Blood of left ventricle • • April, 2006 DLCook Volume Pressure Temperature Flow Duke 06 e. ppt 1

OPB — Physical property taxonomy Blood of left ventricle • • April, 2006 DLCook Volume Pressure Temperature Flow Duke 06 e. ppt 2

OPB — Each OPB entity has a UID OPB: Fluid pressure April, 2006 DLCook Duke 06 e. ppt 3

Annotation — UID of a property is a duple of OPB and FMA UIDs OPB: Fluid pressure. FMA: Blood of left ventricle • • April, 2006 DLCook Volume Pressure Temperature Flow Duke 06 e. ppt 4

Appl. Model Ontology schema can represent JSim models Knowledge resource FMA: relation FMA has relation FMA: entity OPB: property JSim code annotated with OPB. FMA UIDs JSim: var JSim model JSim: equ April, 2006 DLCook Duke 06 e. ppt 5

Appl. Model Ontology schema can represent JSim models Knowledge resource FMA: relation Appl. Model Built in Protégé (like FMA, OPB, etc. ) FMA has relation FMA: entity OPB: property JSim: var JSim model JSim: equ April, 2006 DLCook Duke 06 e. ppt 6

Appl. Model Ontology schema can represent JSim models Knowledge resource FMA: relation Appl. Model relation has relation FMA: entity individual has property OPB: property has magnitude JSim: var value Appl. Model component Appl. Model relation JSim: equ April, 2006 DLCook dependency Duke 06 e. ppt UID reference 7

Appl. Models can map to data resources Knowledge resource Knowledge model URI: relation Relation has relation is related to Computational model Data resource Individual URI: entity URI: data has property is property of URI: property Property represented as has magnitude is magnitude of URI: variable Magnitude value of depends on knowledge element data structure refers to URI: operator April, 2006 Dependency DLCook Duke 06 e. ppt Value Model component Model relation 8