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

PeerJ

article

Gaurav Vaidya¹  Nico Cellinese²  Hilmar Lapp⁴ 

[1] Renaissance Computing Institute ,(RENCI), University of North Carolina at Chapel Hill;Florida Museum of Natural History, University of Florida;Informatics Institute, University of Florida;Department of Biostatistics and Bioinformatics, Duke University

关键词: Phylogenetics;    Data standard;    Clade definitions;    JSON-LD;    Computational semantics;    Data curation;    Semantic web;   

DOI  :  10.7717/peerj.12618

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY