Updated model for taxonomic units

[gaurav]

Previously, taxonomic units (TU) were identified based on the properties they had: a TU with a scientific name referred to a taxon, one with an occurrence ID referred to a specimen, and so on. A single TU was also allowed to have multiple scientific names or multiple occurrence IDs. This meant that you could represent a huge variety of taxonomic units, but it also meant that figuring out what a particular TU actually meant could be really complicated. Designing a user interface that could handle all this complexity was also a challenge.

Instead, I propose that we simplify taxonomic units so that each taxonomic unit must have a single type (stored in the JSON-LD @type property), indicating whether they are taxon concepts (with or without a citation) or specimens. This will also make it easier to add taxonomic units for apomorphies and phylorefs later on.

In the Phyx and the OWL/JSON-LD file, this will look like this:

{
  "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
  "nameString": "Diplocynodon ratelii",
  "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107"
}

One nice this about this approach is that this is pretty readable both as annotations and in the class expression in Protege.

(This example doesn't have the nomenclatural code, since I need to figure out how to add that on the phylogeny!)

You can also provide a more detailed description if you need to using the TDWG Taxon Concept ontology, such as including original descriptions or circumscription information (i.e. the accordingTo, sensu or sec):

{
  "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept",
  "hasName": {
    "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName",
    "label": "Diplocynodon ratelii Pomel, 1847",
    "nameComplete": "Diplocynodon ratelii",
    "genusPart": "Diplocynodon",
    "specificEpithet": "ratelii",
    "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000036"
   },
   "label": "Diplocynodon ratelii Pomel, 1847 sec Díaz Aráez et al, 2017",
   "describedBy": { Citation to Pomel, 1847 },
   "accordingTo": { Citation to Díaz Aráez et al, 2017 }
}

What do you think?