Replace NCBI taxon ID integer with ontology term

[david4096]

In #612 I mentioned the inconsistency in representing the NCBI taxon ID as an integer on a reference when the biometadata objects use an Ontology term. This PR closes #612 by replacing the NCBI taxon ID int32 with an ontology term.

[mbaudis]

-1 on this in the current implementation.

Species is defined inbio_metadata.Individual.species

So this should be a reference to the individual (or a copy of the same structure, as a fudge; i.e. OntologyTerm species instead of OntologyTerm ncbi_taxon_id).

  // For a representation of an NCBI Taxon ID as an OntologyTerm, see
  // NCBITaxon Ontology
  //   http://www.obofoundry.org/ontology/ncbitaxon.html
  // For example, 'Homo sapiens' has the ID 9606. The NCBITaxon ontology ID for
  // this is NCBITaxon:9606, which has the URI
  // http://purl.obolibrary.org/obo/NCBITaxon_9606
  OntologyTerm species = 7;

[david4096]

Thanks @mbaudis, that makes sense I've changed the field to be named species.

[mbaudis]

+1 (and removal of the -1 above)

[david4096]

Updated to include using an Ontology Term on reference sets as well. Thanks @ejacox !

[david4096]

Implemented in the server here, and client with demonstrated tests in compliance.