Effectopedia is an open-knowledge aggregation and collaboration tool designed to facilitate the interdisciplinary efforts for delineating adverse outcome pathways (AOPs) in an encyclopedic manner with greater predictive power. 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 experiments and apply 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 for 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 for experts with similar interest in a specific toxicity pathways.
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.
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 alpha release of Effectopedia is 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.
Effectopedia is distributed under GNU General Public License for free. The most recent version of the source is available at Sourceforge.
You can use the link below to download the current alpha version of Effectopedia and the corresponding release notes.
You can use our sourceforge.net donation page to make general contributions toward Effectopedia development. In the near future we plan to introduce our Features Auction which will enable you or your organization to make targeted donations in order to influence the priority for implementation certain features which you might find very useful for your work.
You can follow the development of Effectopedia on or become part of our group