Information in Regnum that should be included in the Clade Ontology

[gaurav]

I'm using this issue to make a list of all the fields currently available in Regnum that we might want to include into the Clade Ontology. When I write the conversion scripts, I'll include all this information in the PHYX file. We should assume that we are going to include all this information in the Clade Ontology, unless there's a good reason not to. I'll close this issue once all this information is in the Clade Ontology.

For testing the phyloreferences in the Curation Tool, we need:

• Clade definition label/name
• Clade definition
• Specifier information, including:
  • Verbatim specifier
  • Type of specifier: internal or external
  • Type of taxonomic unit: taxon name (including authority), specimen identifier or URI
• The primary reference phylogeny (once we close Make it clear that Reference Phylogeny information can be added to the Curator Notes field klados#70) and additional reference phylogenies (once we close Replace "Study metadata" with the ability to add citations directly to phylogenies and phyloreferences klados#96)
• Does this clade definition point to a crown clade or a total clade? (once we close Remind users to note whether a clade definition specifies a crown clade in the verbatim definition klados#71)
• The qualifying clause (once we close Add a field for a verbatim qualifying clause klados#112)

Additional metadata that can be imported includes:

• Regnum registration number
• Definitional authors for the clade definition
• Citation for the clade definition
• If the clade name is a pre-existing name under an existing nomenclatural code:
  • The code (ICZN, ICNafp, Bacteriological) under which the name was created
  • Citation for the pre-existing name, including nominal authors
• Specifier information, including:
  • Whether the specifier points to an extinct or extant species
  • The nomenclatural code under which the species name was created
  • The uBio ID, NCBI ID or Treebase ID for the species name
• Abbreviated clade definition