Biochemical Situational Modeling:Dumontier:OWLED2008 1 Situational Modeling: Defining Molecular Roles in Biochemical Pathways and Reactions Michel Dumontier, PhD Assistant Professor of Bioinformatics Department of Biology, School of Computer Science, Institute of Biochemistry, Ottawa Institute of Systems Biology Carleton University
11
Embed
Situational Modeling: Defining Molecular Roles in Biochemical Pathways and Reactions
Central to a coherent understanding of cellular biology is a faithful representation of biochemical processes as it pertains to its molecular participants. Current representations underspecify our knowledge because they fail to indicate the roles of the molecular components during relevant processes. Here, we describe a knowledge representation using OWL2 that overcomes previous limitations in modeling biochemical events and has clear implications for the accurate functional/role based annotation of molecular components.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Glucose is a Substrate in GKR– Mixing of types (natural vs role) makes ontology harder to maintain– OWL binary predicates disallow reification– Represented as a class restriction wouldn’t be universally true
• Approach– Represent knowledge from the event perspective
GKR involves Glucose as a Substrate– Vague – could be substrate in any number of other reactions. Need a temporal
pivotGKR realizes the Substrate Role held by Glucose
– We don’t want to talk about roles, but fully defined roleplayersA Substrate is an Object that holds the Substrate Role
• Class based representation– Use of N&S conditions aims to classify instances– Roles are pivot that must be instantiated and realized– Role chains bypass pivots, and makes queries more natural
• Inspired by Basic Formal Ontology (BFO)– Some disagreement on treatment of role/function
• We can currently ask in what reaction is glucose a substrate, but we can`t ask which molecules are substrates (because not every member of the class is).– P4 has this useful class usage feature...
Wacky Idea: querysome (Glucose and Substrate)and getGlucose that isBearerOf some SubstrateRole that isRealizedBy