Streamlined and improved taxonomic units

[gaurav]

This PR cleans up taxonomic units in several ways:

• Taxonomic units have clear types (stored in the @type property), indicating whether they are taxon concepts (with or without a citation) or specimens, allowing us to more easily add taxonomic units for apomorphies and phylorefs later on. (closes Updated model for taxonomic units #20).
• RDF properties used by taxon concepts and names have been rewritten to bring them more into line with the TDWG ontologies TaxonConcept and TaxonName, including the use of TaxonName:nameComplete instead of dwc:scientificName (closes Add support for generating canonical name #8).
• External references are stored in the @id element rather than in a separate property.
• Added support for nomenclatural codes in scientific names (as per Record nomenclatural code with scientific names klados#143). Note that this PR includes an earlier version of the nomenclature code system; this is updated and improved in Improve nomenclatural code implementation in TaxonNameWrapper #26.

This PR also introduces a new TaxonConceptWrapper as an analogue to SpecimenWrapper and renames the ScientificNameWrapper to the shorter TaxonNameWrapper.

This PR should be merged after #21 has been reviewed and merged.

[hlapp]

I guess my main confusion here is whether and why you are synonymizing occurrence IDs and specimen IDs.

[hlapp]

So you are treating occurrence ID and specimen ID as synonymous here? I feel like I must be missing something.

[gaurav]

We previously recorded specimen identifiers as Darwin Core Triplets at three separate fields (institutionID, collectionID, catalogNumber), but I figured in this PR that it made sense to combine them into a single field so that they could be edited more easily from the Curation Tool. I was pretty sure based on its documentation that dwc:occurrenceID was the right way of do this. I've also just recorded some examples of other data providers using this model in phyloref/clade-ontology#61 (comment).

I should definitely use dwc:basisOfRecord to make it clear that this is a specimen, not just any occurrence, but apart from that I'm not sure what other field we could use to store the specimen ID here. Am I forgetting some property that I should use instead?

[gaurav]

I've just added dwc:basisOfRecord entries to specimens in this PR so they're no longer pure occurrence IDs. Should I merge this PR while we discuss the basis way of representing specimens in phyloref/clade-ontology#61 (comment)? Otherwise, I could take out specimens entirely from this PR and then we could put them back in once we have a better plan to implement them.

[hlapp]

Nothing objectionable here right now. I guess we'd have to look at and review the output to come to a more full conclusion as to whether this is the right way of doing it.