Products generated by this project, including publications, presentations, software, and data sets.


  • Klados: Web-based tool for curating published phylogenetic clade definitions to machine-readable phyloreferences (in Phyx files).
  • phyx.js: Javascript library for manipulating Phyx files (and converting them to OWL ontologies). (NPM release)
  • phylo2owl: Tool to convert phylogenies to OWL ontologies.


  • Vaidya G, Cellinese N, Lapp H. (2022). A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 doi:
  • Cellinese, N., Conix, S., Lapp, H. (2022). “Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts”, Philosophy, Theory, and Practice in Biology 14: 7. doi:
  • Vaidya G., Cellinese N., Lapp H. (2021). JPhyloRef: a tool for testing and resolving phyloreferences. Journal of Open Source Software, 6(64), 3374,
  • Eberhart A., Carral D., Hitzler P., Lapp H., Rudolph S. Seed Patterns for Modeling Trees. In: Advances in Pattern-Based Ontology Engineering. IOS Press; 2021. pp. 48–67.
  • David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph. On the Ontological Modeling of Trees. In: Proceedings of the 8th Workshop on Ontology Design and Patterns, WOP 2017, co-located with the 16th International Semantic Web Conference, ISWC2017, Vienna, Austria, October 2017. Also on arXiv, arXiv:1710.05096 [cs.AI].

Presentations and posters