TY - GEN
T1 - Argumentation to represent and reason over biological systems
AU - Wyner, Adam
AU - Riley, Luke
AU - Hoehndorf, Robert
AU - Croset, Samuel
PY - 2012
Y1 - 2012
N2 - In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena. To represent and reason with inconsistency as well as provide explanation, we represent a fragment of a biological system and its interactions in terms of a computational model of argument and argumentation schemes. Process pathways are represented in terms of an argumentation scheme, then abstracted into a computational model for evaluation, yielding sets of 'consistent' arguments that represent compatible biological processes. From the arguments, we can extract the corresponding processes. We show how the analysis supports explanation and systematic exploration in a biology network.
AB - In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena. To represent and reason with inconsistency as well as provide explanation, we represent a fragment of a biological system and its interactions in terms of a computational model of argument and argumentation schemes. Process pathways are represented in terms of an argumentation scheme, then abstracted into a computational model for evaluation, yielding sets of 'consistent' arguments that represent compatible biological processes. From the arguments, we can extract the corresponding processes. We show how the analysis supports explanation and systematic exploration in a biology network.
KW - argumentation
KW - computational methods
KW - systems biology
UR - http://www.scopus.com/inward/record.url?scp=84865574670&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-32395-9_10
DO - 10.1007/978-3-642-32395-9_10
M3 - Conference contribution
AN - SCOPUS:84865574670
SN - 9783642323942
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 124
EP - 138
BT - Information Technology in Bio- and Medical Informatics - Third International Conference, ITBAM 2012, Proceedings
T2 - 3rd International Conference on Information Technology in Bio- and Medical Informatics, ITBAM 2012
Y2 - 4 September 2012 through 5 September 2012
ER -