There are three repositories we should consider archiving:

1. The phylo2owl repository (https://github.com/phyloref/phylo2owl) contains a Python script that uses a template-based approach to converting phylogenies (in Newick, Nexus or NeXML formats) into OWL in RDF/XML. We haven’t updated this code since July 2018. Phyx.js can convert Newick phylogenies into OWL in JSON-LD or Turtle by itself, and we could add support for importing phylogenies in Nexus or NeXML if we need to.

2. The vocab repository (https://github.com/phyloref/vocab) was intended to contain any vocabularies and ontologies we would develop for this project, but we ended up putting our vocabularies into the phyloref-ontology repository (https://github.com/phyloref/phyloref-ontology, from where it is accessible on ontology.phyloref.org) and the Clade Ontology will eventually be hosted at https://github.com/phyloref/clade-ontology, so I don’t think we need this repo any longer.

3. We put an early draft of the Phyloref specification to the specification repository (https://github.com/phyloref/specification), but I’m not sure if we need this separate from what we’ve already covered in the Phyx.js. If so, or if we’re unsure, we can leave this repository around without any problem, since it contains only Markdown files and so will not receive security advisories.