TPT taxonomy - assume that when acceptedNameUsage is populated that the name is a synonym

jhpoelen commented 1 year ago

E.g.,

echo -e "\tBrueelia subalbicans" | nomer append tpt

currently produces:

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Brueelia subalbicans	HAS_ACCEPTED_NAME	5516	Brueelia subalbicans	Piaget, 1885	species		Animalia \| Arthropoda \| Insecta \| Psocodea \| Troctomorpha \| Nanopsocetae \| Phthiraptera \| Ischnocera \| Philopteridae \| Brueelia \| subalbicans		kingdom \| phylum \| class \| order \| suborder \| infraorder \| parvorder \| nanorder \| family \| genus \| specificEpithet
	Brueelia subalbicans	HAS_ACCEPTED_NAME	5517	Brueelia subalbicans		species		Animalia \| Arthropoda \| Insecta \| Psocodea \| Troctomorpha \| Nanopsocetae \| Phthiraptera \| Ischnocera \| Philopteridae \| Brueelia \| subalbicans		kingdom \| phylum \| class \| order \| suborder \| infraorder \| parvorder \| nanorder \| family \| genus \| specificEpithet

but in TPT taxonomy , the accepted name usage ID point to 1032 (internal id) - which refers to:

Brueelia papuana (Giebel, 1879)

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Brueelia papuana	HAS_ACCEPTED_NAME	1032	Brueelia papuana	(Giebel, 1879)	species		Animalia \| Arthropoda \| Insecta \| Psocodea \| Troctomorpha \| Nanopsocetae \| Phthiraptera \| Ischnocera \| Philopteridae \| Brueelia \| papuana		kingdom \| phylum \| class \| order \| suborder \| infraorder \| parvorder \| nanorder \| family \| genus \| specificEpithet

jhpoelen commented 1 year ago

@EMTuckerLab suggested to simply say: the taxonomicStatus column for the entire dataset Phthiraptera is empty.

e.g., Brueelia subalbicans .

jhpoelen commented 1 year ago

after changes made via https://github.com/globalbioticinteractions/nomer/commit/f22bf837d5f595eb597deaf5b5aaaf5f99c6c7af

the command:

echo -e "\tBrueelia subalbicans" | nomer append tpt

now produces:

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Brueelia subalbicans	SYNONYM_OF	1032	Brueelia papuana	(Giebel, 1879)	species		Animalia \| Arthropoda \| Insecta \| Psocodea \| Troctomorpha \| Nanopsocetae \| Phthiraptera \| Ischnocera \| Philopteridae \| Brueelia \| papuana		kingdom \| phylum \| class \| order \| suborder \| infraorder \| parvorder \| nanorder \| family \| genus \| specificEpithet
	Brueelia subalbicans	SYNONYM_OF	1032	Brueelia papuana	(Giebel, 1879)	species		Animalia \| Arthropoda \| Insecta \| Psocodea \| Troctomorpha \| Nanopsocetae \| Phthiraptera \| Ischnocera \| Philopteridae \| Brueelia \| papuana		kingdom \| phylum \| class \| order \| suborder \| infraorder \| parvorder \| nanorder \| family \| genus \| specificEpithet

Note that now Brueelia subalbicans are associated as synonyms of Brueelia papuana .

jhpoelen commented 1 year ago

That that two record of the name do appear to exist -

$ curl --silent -L https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Phthiraptera/Phthiraptera-standardized-v2.csv | grep "Brueelia subalbicans"
TPT_v1,5516,,1032,,,,,,"Brueelia subalbicans  Piaget, 1885",,,,,,,,Animalia,Arthropoda,Insecta,,,Psocodea,Troctomorpha,Nanopsocetae,Phthiraptera,Ischnocera,,Philopteridae,,,,Brueelia,,subalbicans,,species,," Piaget, 1885",,,,,,Brueelia subalbicans
TPT_v1,5517,,1032,,,,,,Brueelia subalbicans ,,,,,,,,Animalia,Arthropoda,Insecta,,,Psocodea,Troctomorpha,Nanopsocetae,Phthiraptera,Ischnocera,,Philopteridae,,,,Brueelia,,subalbicans,,species,,,,,,,,Brueelia subalbicans

globalbioticinteractions / nomer

TPT taxonomy - assume that when acceptedNameUsage is populated that the name is a synonym #138