Phenoscape has mentored, under the auspices of NESCent, another Google Summer of Code student this year. Kasia Hayden developed a plugin package for Mesquite that allows users to view character matrices and EQ (ontology-based) annotations produced using the Phenex tool. The primary purpose was to allow curators to share their annotation work with others in the context of a more familiar tool. Users can select cells in a Mesquite character matrix and, using two new cell tools, see EQ annotations either as text in the bottom pane of the matrix window, or as a graph in a separate pop-up window.
This project also served as an important use-case for the NeXML phylogenetics exchange language. Although Phenex has used NeXML for over a year, the annotations it generated were not readable by the NeXML package for Mesquite. During and after the database interoperability hackathon last spring, the NeXML developers worked out a standard for annotation and a common java library for parsing NeXML. Kasia’s project served as a test of that interoperability, and the final product demonstrates that we have achieved it.
Although I was the primary mentor for this project, it would not have been possible without the contributions of Jim, who was co-mentor and who made some Phenex changes to support us, or of Rutger Vos, who pulled the annotation format together and provided us with lots of advice on the NeXML language and library implementation.
Finally, check out Kasia’s walk through of the project. Her blog also traces the progress and frustrations of learning about ontologies, Mesquite, NeXML and the GraphViz Dot language, all in one summer. Thank you Kasia!
Phenoscape 