Software
- 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.
Publications
- 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: https://doi.org/10.7717/peerj.12618
- 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: https://doi.org/10.3998/ptpbio.2101
- Vaidya G., Cellinese N., Lapp H. (2021). JPhyloRef: a tool for testing and resolving phyloreferences. Journal of Open Source Software, 6(64), 3374, https://doi.org/10.21105/joss.03374
- 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. http://ceur-ws.org/Vol-2043/. Also on arXiv, arXiv:1710.05096 [cs.AI].
Presentations and posters
- Cellinese, Vaidya, Lapp (2021) Life in the digital world: a journey from RegNum to phyloreferences. Presentation at the Botanical Society of America Meeting (virtual).
- Vaidya, Lapp, Cellinese (2020) “Enabling Machines to Integrate Biodiversity Data with Evolutionary Knowledge.” Presentation at TDWG 2020 (virtual).
- Cellinese & Vaidya (2019) All the clades in the world: how to navigate in tree space. Presentation and Workshop at the Systematic Biology Meeting, Gainesville, FL.
- Lapp H (2019) “Of Trees and Owl: The challenges of reasoning over the semantics of shared descent.” Presentation at US2TS 2019, Durham, NC.
- Vaidya G, Lapp H, Cellinese N (2019) “Building an ontology of logic definitions for groups of biological organisms to enable data integration.” Poster at US2TS 2019, Durham, NC.
- Vaidya G, Lapp H, Cellinese N (2018) “All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions.” Presentation at TDWG 2018, Dunedin, New Zealand. (slides)
- Vaidya G, Lapp H, Cellinese N (2016) “Creating computable definitions for clades using the Web Ontology Language (OWL).”
Presentation at TDWG 2016, Santa Clara de San Carlos, Costa Rica. (video; ours is the second talk in that session, starting at around 16:30) - Vaidya G, Lapp H, Cellinese N (2016) “The Semantic Clade.” Presentation at the 2016 Evolution Meetings, Austin TX. (video)
- Cellinese N, Lapp H (2016) “Integrating data with phylogenies, at scale.” Presentation at the Final Phenotype RCN Summit, held on February 26-28 at Biosphere2 in Arizona.
- Cellinese N, Lapp H (2015) “Integrating data at the Tree of Life scale using computable clade definitions.” Presentation at the 2015 International Union of Biological Science Meeting in Berlin, Germany.
- Cellinese N, Lapp H (2015) “An ontology-based system for querying Life in a post-taxonomic age.” Presentation at the 2015 TDWG Meeting in Nairobi, Kenya.