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

Publication ,  Journal Article
Vaidya, G; Cellinese, N; Lapp, H
Published in: PeerJ
January 2022

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.

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Published In

PeerJ

DOI

EISSN

2167-8359

ISSN

2167-8359

Publication Date

January 2022

Volume

10

Start / End Page

e12618

Related Subject Headings

  • Software
  • Semantics
  • Records
  • Phylogeny
  • Biology
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

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Vaidya, G., Cellinese, N., & Lapp, H. (2022). A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ, 10, e12618. https://doi.org/10.7717/peerj.12618
Vaidya, Gaurav, Nico Cellinese, and Hilmar Lapp. “A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).PeerJ 10 (January 2022): e12618. https://doi.org/10.7717/peerj.12618.
Vaidya, Gaurav, et al. “A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).PeerJ, vol. 10, Jan. 2022, p. e12618. Epmc, doi:10.7717/peerj.12618.

Published In

PeerJ

DOI

EISSN

2167-8359

ISSN

2167-8359

Publication Date

January 2022

Volume

10

Start / End Page

e12618

Related Subject Headings

  • Software
  • Semantics
  • Records
  • Phylogeny
  • Biology
  • 11 Medical and Health Sciences
  • 06 Biological Sciences