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

Loading...
Thumbnail Image

Date

2022-01

Journal Title

Journal ISSN

Volume Title

Repository Usage Stats

13
views
8
downloads

Citation Stats

Abstract

To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.

Department

Description

Provenance

Citation

Published Version (Please cite this version)

10.7717/peerj.12618

Publication Info

Vaidya, Gaurav, Nico Cellinese and Hilmar Lapp (2022). A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ, 10. p. e12618. 10.7717/peerj.12618 Retrieved from https://hdl.handle.net/10161/26575.

This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.


Unless otherwise indicated, scholarly articles published by Duke faculty members are made available here with a CC-BY-NC (Creative Commons Attribution Non-Commercial) license, as enabled by the Duke Open Access Policy. If you wish to use the materials in ways not already permitted under CC-BY-NC, please consult the copyright owner. Other materials are made available here through the author’s grant of a non-exclusive license to make their work openly accessible.