//localhost:4321/key-objective-1/index.html Hugo en //localhost:4321/key-objective-1/agatashakira-the-aop-project-part1/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:4321/key-objective-1/agatashakira-the-aop-project-part1/index.html The AOP project ► Key objective 1 Author: Shakira Agata This Jupyter Notebook describes the steps needed to create the preliminary table that is needed for construction of an AOP network that focuses on inflammatory processes in human organ systems. This notebook focuses on the organ systems: brain, liver, kidney and lung due to research interests of the author. The preliminary table will contain the following information: AOP (adverse outcome pathway), AOP title, KE name (key event name), AO (adverse outcome), AO title, KER (key event relationship), KER ID and title of the organ system. To achieve this result, three SPARQLqueries will be executed against AOP-Wiki RDF to extract the AOPs that are related to inflammatory processes along with their respective upstreamKEs, downstreamKEs and KERs. The detailed steps are outlined in the following eight sections: //localhost:4321/key-objective-1/agatashakira-the-aop-project-part2/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:4321/key-objective-1/agatashakira-the-aop-project-part2/index.html The AOP project ► Key objective 1 Author: Shakira Agata This Jupyter notebook describes the steps needed to construct an AOP network that focuses on inflammatory processes in human organ systems AOP network. Briefly the nodetable and edgetable were defined followed by construction of the AOP network and adaptation of the visual style with py4cytoscape. Py4cytoscape is a Python package that collaborates with Cytoscape for visualization of molecular networks and biological pathways. The detailed steps are outlined in the following eight sections: //localhost:4321/key-objective-1/agatashakira-the-aop-project-part3/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:4321/key-objective-1/agatashakira-the-aop-project-part3/index.html The AOP project ► Key objective 1 Author: Shakira Agata This Jupyter notebook describes the steps needed to enrich your AOP network by addition of molecular pathways from WikiPatwhays and genes through CyTargetLinker. This notebook is dependent on the output: ´Agata,completenodetable.xlsx´ which contains the KE-WP mapping results. This notebook is subdivided into the following ten sections: Section 1: KE-WP mapping Section 2: Importing the tables needed to construct the node table and edge table Section 3: Loading the node table and edge table Section 4: Defining the node table and edge table Section 5: Construction of the molecular AOP network Section 6: Adaptation of stylistic aspects of the molecular AOP network Section 7: Extension of the molecular AOP network using Cytargetlinker and WikiPathways linkset Section 8: Changing the visual style of CytargetLinker-extended molecular AOP ntwork Section 9: Saving results Section 10: Metadata Section 1: System preparation In this section, you will install the necessary packages for this notebook.