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Saturday, December 22, 2018

New paper: "Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials"

An adverse outcome pathway (AOP) links
molecular initiating events (MIEs) via key
events (KEs) to the adverse outcome (AO).
Each event is a biological process and it should
be able to link them to normal biological
pathways (PWs). Figure from the paper.
Marvin Martens published his vision on the integration of adverse outcome with biological pathways (doi:10.3389/fgene.2018.00661). Specifically, he looked into our options to link the AOPWiki with WikiPathways, taking input from various people around the world (see the list of co-authors). The paper looks into how links can be made, and some statistics are calculated for genes mentioned in AOPs and biological pathways, as well as seeing which molecular initiators are found in biological pathways (see the figure on the right).

The paper started out as positioning paper but I was happy to see that Marvin could not resist getting some actual data and include that as well. With the code available from GitHub and archived on Zenodo (doi:10.5281/ZENODO.1306408). The next step is to formalize this integration, and the first bits of data are being produced and they look very exciting!

BTW, if you like where this is going, also make sure to read this paper by Dr. Penny NymarkA Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions).

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