expose taxonomic hierarchy inference made by GBIF parser

[jhpoelen]

GBIF parser infers taxonomic hierarchy by the structure of a scientific name when possible.

E.g.,

Andrena (Aenandrena) aeneiventris Morawitz, 1872

likely refers a taxonomic name by Morawitz, 1872 of genus Andrena, with subgenus (or infragenericEpithet), and specificEpithet aeneiventris.

Suggest to extend Nomer to include these taxon hierarchy inferences in gbif-parse matcher.

[jhpoelen]

related to #134

@seltmann @jtmiller28 Would you say that infragenericEpithet is equivalent to subgenus ?

[jhpoelen]

previously,

echo -e "\tAndrena (Aenandrena) aeneiventris Morawitz, 1872"\
 | nomer append gbif-parse

yielded

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Andrena (Aenandrena) aeneiventris Morawitz, 1872	SAME_AS		Andrena aeneiventris	Morawitz, 1872

but now, the results are:

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Andrena (Aenandrena) aeneiventris Morawitz, 1872	SAME_AS		Andrena aeneiventris	Morawitz, 1872	species		Andrena | Aenandrena | aeneiventris		genus | infragenericEpithet | specificEpithet

Note that resolvedRank, rsolvedPath etc. are now populated.

[jtmiller28]

@jhpoelen Yep I would agree, that would match the infraSpecificEpithet standard in the dwc. @seltmann probably has more experience in this regard though if there is some standard I am unaware of.

[jhpoelen]

@jtmiller28 thanks for your note. Did you see that the GBIF rank description was infragenericEpithet not infraspecificEpithet ? Just making sure that I communicated my question as intended.

[jhpoelen]

Note that DwC has both

https://dwc.tdwg.org/terms/#dwc:subgenus

and

https://dwc.tdwg.org/terms/#dwc:infragenericEpithet

[jtmiller28]

I knew of the infraSpecificEpithet, but was unaware of the infragenericepithet field being currently in dwc. I was more meaning that it makes sense to me given the current conventions that anything that categorizes genuses without going to specificEpithet field (I.e. subgenus and the like) would be included a field called infragenericepithet.

Does gbif contain this field? I know they follow dwc standards, but presently haven't seen a case where subgenus is correctly parsed in a name.

[jhpoelen]

Closing issue; functionality has been added and made available in Nomer release.