beyond ontologies frank d. russo, ph.d. waycraft biosoftware iscb rocky ‘06
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Beyond Ontologies
Frank D. Russo, Ph.D.
WayCraft Biosoftware
ISCB Rocky ‘06
WayCraft Biosoftware 1 Dec 2006Frank D. Russo
Metadata-driven Modeling
• Semi-structured, very flexible• RDF, DAML-OIL, Frame-Slot• Excellent for classification, and for
cataloguing and describing concepts• GO / OBO, UMLS, many others
Term
Term
Term
Subject Predicate Object
WayCraft Biosoftware 1 Dec 2006Frank D. Russo
“We need a theoretical framework in which to embed biological data so that the endless stream of data, filled with the flotsam and jetsam of evolution, can be sifted and abstracted.”
Sidney BrennerThe Scientist, 16[6]:12, Mar 18th, 2002
More Than a Name
WayCraft Biosoftware 1 Dec 2006Frank D. Russo
Implicit Objects and Relationships
E
S
ES
A biologist writes:
… and implies:
MolecularComplex
ES
Protein
E
Compound
S
Composition
MolecularComplex
ES
Protein
E
Compound
S
Reaction
E-S Binding
Process
Protein
Etot
Protein
E
MolecularComplex
ES
Generalization
comp form
WayCraft Biosoftware 1 Dec 2006Frank D. Russo
Levels of Abstraction
A B
A R B
Function
MechanismATP
A
R0
Bf
Rp
RB
ADP
WayCraft Biosoftware 1 Dec 2006Frank D. Russo
Disease Cards Application