NSF DBI-1458604 Collaborative Research: ABI Innovation: An Ontology-Based System for Querying Life in a Post-Taxonomic Age

Project website


Improving our understanding of life, whether the biology of individual species such as our own, or the mechanisms and processes governing biodiversity at large, critically depends on integrating, querying, and aggregating biological data from many different organisms. To this day, the most fundamental and common way to accomplish this relies on organism names, making these, one of the pillars of querying and managing our biological knowledge and data. However, the traditionally used names for organisms and groups of organisms, which are based on Linnaean nomenclature, suffer from two major limitations to their usefulness when it comes to integrating and communicating data. First, because they are simple text-strings, the meaning intended by those who coin a name and those who apply it is inaccessible to machines.

As a result, exactly which organisms a name is or is not meant to include is often ambiguous, and names are therefore often applied inconsistently. Second, there are many groups of organisms that do not yet and may never have a Linnaean name, but for which molecular or macroscopic characteristics have been discovered that constitute valuable biological knowledge. This project aims to address these issues by generating a mechanism, called phyloreferencing, that allows referring to any group of organisms of shared evolutionary descent by a machine-interpretable definition of the unique pattern of descent that distinguishes the group from all others. With the recent synthesis and continuous update of a universal phylogenetic Tree of Life, phyloreferences will have immediate and broad practical applications for communicating, integrating, and querying biological data across the Tree of Life.

Cellinese, N., Conix, S., Lapp, H. 2022. Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon ConceptsPhilosophy, Theory and Practice in Biology 14: doi.org/10.3998/ptpbio.2101

Vaidya, G., Cellinese, N., Lapp, H. 2022. A new phylogenetic data standard for computable clade definitions: The Phyloreference Exchange Format (Phyx). PeerJ, In Press.

Vaidya, G., Cellinese, N., Lapp, H. 2021. JPhyloRef: a tool for testing and resolving phyloreferences. Journal of Open Source Software doi:10.21105/joss.03374.


Related topics:

Cellinese, N., Baum, D.A., Mishler, B.D. 2012. Species and Phylogenetic Nomenclature. Systematic Biology 61: 885-891.

Parr, C. S., Guralnick, R., Cellinese, N., Page, R.D.M. 2012. Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology & Evolution 27: 94-103.