The Phyloreference Exchange (PHYX) format is a JSON representation that can be used to store and transfer definitions of phyloreferences. This library provides classes to help interpret some parts of these files, and for transforming an entire Phyx file into a JSON-LD representation that can be reasoned over with an OWL 2 DL reasoner. See the Phyloreference Curation Tool or the Clade Ontology for examples of its usage.
You can install phyx.js using npm:
$ npm install @phyloref/phyxTutorials demonstrating the use of phyx.js are available.
phyx.js should be cited by citing our publication documenting the Phyx format and phyx.js.
Vaidya G, Cellinese N, Lapp H. 2022. A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx) PeerJ 10:e12618 doi:10.7717/peerj.12618
Funded by the US National Science Foundation through collaborative grants DBI-1458484 and DBI-1458604. See Funding for details.