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!

You might wonder why this has taken almost a year since we launched Phenoscape in June 2007.  The reason is that until just recently our software as well as ontology development activities have built on existing projects (such as Phenote on the software side or PATO on the ontology side) that already had their community infrastructure, or given rise to new community ontologies (such as the TAO and TTO) that each received their infrastructure within the OBO umbrella.

However, as we start shifting our focus this summer to developing the database and web-based user interface for the EQ data our curators will soon be generating in increasing amounts, our own code repository will be the natural home for much of the code we’ll develop.