AOP-XML: an exchange format for toxicological pathways
Knowledge about adverse outcome pathways — how an initial molecular interaction leads through intermediate steps to a harmful effect — sat in several databases that could not read each other. We designed the format that connects them.
- Document architecture based on OECD Harmonised Template 201, agreed with the responsible expert group and with the knowledge base development team
- Implementation as an XML Schema Definition, version-controlled and ready for handover to a repository under the client's control
- Java reference application that generates valid documents from domain data, delivered with open source code
- Validator in three forms — console application, desktop tool and web service — so that data providers can check files before submitting them
- Export application in C#/.NET Core that converts pathway and chemical data from the existing wiki platform into the new format, running on both Windows and Linux and integrable into the web application
- Presentation of the format and resolution of open questions at a working session at the US Environmental Protection Agency offices in Durham, North Carolina, with the resulting changes subsequently implemented
Why this is typical of us: the real work was not writing a schema. It was negotiating a version that several teams with different data models could all work with — and documenting it so that it survives without us.