Using n-layer graph models for representing and transforming knowledge on biological pathways

by Zaynab Hammoud
Doctoral thesis
Date of Examination:2021-03-04
Date of issue:2021-03-16
Advisor:Prof. Dr. Frank Kramer
Referee:Prof. Dr. Edgar Wingender
Referee:Prof. Dr. Stephan Waack
Persistent Address: http://dx.doi.org/10.53846/goediss-8478

 

 

Files in this item

Name:Dissertation.pdf
Size:17.0Mb
Format:PDF
Description:Dissertation

The following license files are associated with this item:

Abstract

English

Currently, the use of prior knowledge on biological pathways in research projects is often a manual process, not well documented and hard to reproduce. The aim of this thesis is the definition and implementation of a multi-layer pathway modeling framework. This includes the theoretical definition of the model, operations and an operational language for transforming model and standard operations, e.g. adding and removing nodes, edges and layers. An n-layer graph with nodes arranged within layers and connected via inter- and intra-layer edges will be used. Operations applicable to pathways will include the addition/removal/modification of layers, nodes and inter- and intra-layer edges. A specific model plus a set of operations (for example, removal of irrelevant nodes/edges and layers) defines an exact view of the integrated pathway knowledge given this set of operations. Interfaces to integrate pathway knowledge from standardized encodings into multi-layer pathways and functions for their visualization will be implemented.
Keywords: Data integration; Multilayer Graph; Graph Theory; Biological Pathways; Leishmaniasis; DrugBank; UniProt; rBiopaxparser; BioPAX; Knowledge Representation; Reproducibility; Interoperability; Complex Networks
 
Statistik