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The Online Encyclopedia of Adverse
Outcome Pathways

What is Effectopedia?

Effectopedia is an open-knowledge and structured platform able to display quantitative information on Adverse Outcome Pathways (AOPs). It is a collaborative tool designed to facilitate the interdisciplinary efforts for delineating AOPs in an encyclopedic manner with greater predictive power.

Adverse Outcome Pathways (AOPs) describe the causal linkages following a chemical stressor and the cascade of biological responses across different levels of biological organization, leading to an adverse outcome over time.

Effectopedia is a tool for visual exploration and development of AOPs compliant with OECD Users’ Handbook.

The AOP diagram in Effectopedia is a core visual structure used to navigate through the content of existing AOPs. The AOP diagram captures the causal linkages between AOP elements in their biological context. All elements can be described in summary on the diagram for the general public, or in greater detail for the experts.

Effectopedia is a tool for building simple quantitative relationships between key events along the AOP using experimental data.

Experimental scientists can report test data and metadata using OECD harmonised templates and subsequently use an interface to derive simple quantitative relationships between data sets.

Effectopedia is a dissemination and collaboration tool for modelers.

Effectopedia allows model developers to build a standard description for their models– facilitating interaction with other models. Experiment designers can also use Effectopedia model description to identify the type of data they need to collect in order to build the model.

As a response to the growing awareness that a paradigm shift in chemical risk assessment is needed, Effectopedia provides a capability to move beyond the last half-century’s phenomenological approach with animal testing to a more mechanistic and hypothesis-driven approach. The 21st-Century shift to more prospective hypothesis generation requires more strategic use of systems biology, QSAR and archived toxicological information in the form of AOPs. Effectopedia is designed as a new technology both to reduce multidisciplinary barriers in the development of AOPs and to integrate AOPs with historical case studies.

Instead of testing an individual chemical in such a way that results apply only in the context of narrow experimental conditions, Effectopedia is being designed to define the conditions under which knowledge can be transferred from a single experiment and applied to other species, levels of biological organization, exposure routes, exposure durations, and chemicals, etc. While the graphical editor of Effectopedia facilitates the delineation of AOPs, a key element for success of this approach is to create a common organizational space that helps scientists in different disciplines to recognize broader applications and value of their work. Effectopedia will identify exactly where special knowledge is needed to quantitatively link biological effects and will aid specialists in creating a larger context for their research.

Effectopedia will create live scientific documents that are instantly open for focused discussions and feedback, whilst giving credit to original authors and reviewers. The wiki element of Effectopedia ensures that review processes are continuous and dynamic. New evidence for a biological effect or pathway segment can be presented immediately, keeping Effectopedia’s information current and providing historical documentation of its evolution.

In order to achieve both human and machine interpretability, Effectopedia will offer a natural language interface that is enhanced through the use of ontology-control algorithms. This interface will use clarifying questions and special tags to define the ontologies while preserving the natural language structure of the AOP element descriptions. Integrating these logical elements into the natural language interface gives Effectopedia users the added advantage of publishing Effectopedia contributions as nanopublications. Since their publications also benefit from more accurate machine translations, both the knowledge and resulting collaboration can spread among different languages.

Role of Effectopedia in the AOP-Knowledge Base (AOP-KB)

Effectopedia is one of the modules of the AOP-KB, recommended for quantitative AOP developers and reviewers. It is connected with other modules of the AOP-KB [Read more at aopkb.org ]

Useful links:

  • OECD AOP Development Programme (link)
  • Users’ handbook (link)

Access to training material for Effetopedia, including videos, introduction tutorial, powerpoint slides (link)

News & Announcements

Effectopedia is a collaborative research platform for knowledge and quantitative data exchange on Adverse Outcome Pathways. In 2016, many features of the software have been refined and beta-tested and now offer stable user-friendly experience, supported by training materials.

Quantitative features enabling scientists to enter dose- and time-response data, and use it to derive response-to-response relationships have been added. Many new functionalities have been introduced facilitating model development and interaction using R, MATLAB or Java. Effectopedia continues to support offline and online workflow allowing users to create and save their AOPS locally and publish them in the centralized database once they rich certain level of maturity or choose to openly collaborate with others and store their progress online.

Current Effectopedia version is downloadable java file and will be used as the basis for an online version under development in 2017.

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Downloads

Standard Edition

For lasting contributions to Effectopedia database use the Standard Edition of the program.

Training Edition

To try  Effectopedia use the training edition of the program, that utilizes a periodically wiped server just for tests.

SourceForge Page

For more download options, offline database and the most recent version of the source code please visit Sourceforge page of the project.

Effectopedia is developed by OECD and distributed under GNU General Public License for free. You can use the links above to download the current version
of Effectopedia and the corresponding release notes.

Training

If you would like to explore Effectopedia at your own pace please consider using our online step by step guides and training materials. Currently for courses are available represented  on our training site. They are represented as large thumbnails click on the one you would like to explore to load the course.

Our courses are hosted using Moodle and provide various options for structuring the content and building more engaging interaction. Please share your experience with us – how can we make these courses more effective learning tool for you?

Effectopedia is an open research platform which relies on contributions from scientific community for both content and features suggestions. Please consider joining us in our efforts to build the tool that fits your needs.

If your group or research project needs additional information or  in person training please  contact us.

AOP Knowledge Base (AOP-KB)

AOP Knowledge Base and Tools 

Effectopedia is part of the OECD’s AOP Knowledge Base suite of tools. Constantly developed and refined, AOP-KB is web- based platform which aims to bring together all knowledge on how chemicals can induce adverse effects, therefore providing a focal point for AOP development and dissemination.

AOPPortal

The e AOP Portal is the main entry point of the AOP Knowledge Base. A search engine, the Portal enables search by key words in AOP titles and key events in the AOP Wiki and Effectopedia platforms. It houses the status of all AOPs in the OECD Work Plan and the official copy of OECD endorsed AOPs.

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The AOP Wiki provides a system that organises, via crowd-sourcing, the available knowledge and published research into a verbal description of individual pathways, using a user friendly Wiki interface. Information on AOP is collected in a qualitative, narrative way.

AOPXplorer drives biological understanding by coupling AOP networks with biological data. Using AOPXplorer, AOPs can be visualized using the AOP Ontology, a community resource updated with AOPs from the AOP-Wiki as well as putative AOPs and disease pathways.

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The Intermediate Effects Database (IEDB) provides a platform where real-life data on Intermediate Effects, triggered by actual chemicals, underpin a chemical agnostic AOP and its Key Events. Data is stored in the internal OECD Harmonised Template for Intermediate Effects (OHT 201).

AOP-XML defines a standard for data exchange between the AOP-KB modules as well as with third-party applications. The deliverable of the AOP-XML project is the AOP-XML schema definition (XSD), which will be published by the OECD as the definitive data standard for AOPs.

Dedication

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Each major release of Effectopedia is being dedicated to leaders in QSAR and computational toxicology who created the foundations for Effectopedia and the vision for relating important chemico-biological interactions directly with the structure of chemicals.

The beta releases of Effectopedia are dedicated to Dr. Albert J. Leo for his leadership in understanding the physical nature of partitioning behavior of chemicals in biological systems, and in establishing octanol/water partitioning (LogP) as a model system. Al Leo established the methods to accurately measure Log P for hydrophobic chemicals and then engineered the databases into the fragment method for calculating LogP directly from chemical structure. When he later computerized the calculation of LogP for tens of thousands of untested chemicals, he enabled all governments to eliminate or control the hazards of most bioaccumulative chemicals used in commerce. Amidst the many efforts by others to improve accuracy, CLOGP and its associated knowledge basis remains the gold standard for partitioning behavior. We hold as example his steadfast enthusiasm for looking deeper into the subtleties of chemical behavior to find the significance of seemingly small structural variations.

Acknowledgment

Effectopedia is developed by the OECD with the financial support from the European Commission

Get In Touch

If you are searching for answers, have suggestions or would like to give the Effectopedia team some feedback, please use the contact form below to reach us. The team will try to assist you resolve your issues.

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