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Creating a Structured AOP Knowledgebase via Ontology-Based Annotations.

Cataia Ives1, Ivana Campia2, Rong-Lin Wang3

  • 1Integrated Systems Toxicology Division, NHEERL, U.S. Environmental Protection Agency, RTP, NC, USA.

Applied in Vitro Toxicology
|July 31, 2018
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Summary
This summary is machine-generated.

This study introduces a computable Adverse Outcome Pathway (AOP) framework by annotating 172 AOPs with ontology terms. This enhances AOP development, computational modeling, and genomics data analysis in toxicology.

Keywords:
Adverse Outcome Pathwaykey eventknowledgebaseontology

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Area of Science:

  • Toxicology
  • Computational Biology
  • Bioinformatics

Background:

  • The Adverse Outcome Pathway (AOP) framework integrates diverse toxicity testing data.
  • Increasing AOP descriptions necessitate computable formats for broader application.

Purpose of the Study:

  • To develop a computable Adverse Outcome Pathway (AOP) framework.
  • To annotate existing AOPs using standardized biological ontologies.

Main Methods:

  • Annotated 172 AOPs from AOP-Wiki (as of Dec 2016) using biological ontologies.
  • Utilized an Event Component (Process, Object, Action) for Key Event (KE) annotation.
  • Applied terms from 14 ontologies and controlled vocabularies.

Main Results:

  • Successfully annotated 685 KEs with 809 Event Components.
  • Established seven conventions for KE annotation via Event Components.
  • Created a computable representation of AOPs.

Conclusions:

  • Enables computational reasoners to assist in AOP development and application.
  • Reduces time for converting qualitative AOPs to computational models.
  • Facilitates visualization and analysis of genomics data within the AOP context.