Phyx format

This is a quick overview of the Phyloreference Exchange (PHYX) format. Every Phyx file is a JSON document in the following structure:

• @context: should be https://www.phyloref.org/curation-tool/json/phyx.json
• phylogenies: A list of phylogenies. Each phylogeny can include:
  • title: A title of the phylogeny.
  • newick: A Newick representation of this phylogeny.
  • additionalNodeProperties: A directory of additional properties to be applied to named nodes on the phylogenies. The key should be the node label, while the value should be a directory containing properties and values to be applied to those nodes. Some possible properties include:
    • expectedPhyloreferenceNamed: The label of the phyloreference that is expected to resolve at this node.
• phylorefs: A list of phyloreferences. Each phyloreference can include:
  • label: A short name for this phyloreference.
  • cladeDefinition: The formal, human-readable definition of this phyloreference.
  • pso:holdsStatusInTime: Provides information on the publication status of this
  • internalSpecifiers: Internal specifiers are currently lists of taxonomic units, but will shortly represent a single taxonomic unit. Each taxonomic unit can contain one or more of:
    • scientificNames: Scientific names included in this specifier. Usually described using scientificName to provide a taxonomic name with authority information.
    • includesSpecimens: Specimens included in this specifier. Usually described using an occurrenceID that includes a specimen identifier.
    • specifierWillNotMatch: Provides a textual explanation of why this specifier could not be matched against any node on any phylogeny during ontology generation.
  • externalSpecifiers: should be in the same format as internalSpecifiers above.