A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)

Area of Science:

• Computational biology
• Biodiversity informatics
• Phylogenetics

Background:

• Data integration in biodiversity science relies on shared entities with assessable semantics.
• Taxon concepts are key linking entities, but traditional names lack precise computational meaning.
• Phylogenetic definitions offer well-defined semantics suitable for computational logic and data integration.

Purpose of the Study:

• To develop a method for transforming natural language phylogenetic definitions into a structured, computable format.
• To enable computationally verifiable and reproducible integration of biodiversity data with large-scale phylogenies.
• To establish a foundation for digitizing and computing with phylogenetic definitions.

Main Methods:

• Development of the Phyloreference Exchange Format (Phyx), a JSON-LD-based data format.
• Creation of the phyx.js software library for computational management of Phyx files.
• Focus on capturing rich metadata for all elements of phylogenetic definitions.

Main Results:

• Phyx provides an interoperable data format for phylogenetic definitions, maintaining semantic integrity.
• phyx.js facilitates the computational management and processing of these definitions.
• The developed tools support the digitization and computational use of phylogenetic definitions.

Conclusions:

• Phylogenetic definitions, when formalized using Phyx, are highly suitable for computational comparative biology.
• This approach enhances data integration, reproducibility, and reusability in biodiversity science.
• Phyx and phyx.js provide a foundational layer for computing with phylogenetic definitions at scale.