add separate columns for aligned taxon ranks and their ids

jhpoelen commented 1 year ago

as suggested by @ljwalker and colleagues Chrissy and Christina -

currently, alignedTaxonPath, alignedTaxonPathIds contains the entire hierarchy, pipe delimited.

suggested keep the path columns and add individual columns for name/id pairs of commonly used taxonomic ranks (kingdom, phylum, etc).

example created by @ljwalker includes:

jhpoelen commented 1 year ago

@ljwalker I made a first attempt to add the separate columns for aligned taxon ranks and their ids. Also, I left the path columns as suggested.

Can you please re-run your names and verify that the columns have been added as suggested?

See example below .

alignedKingdomName	alignedKingdomId	alignedPhylumName	alignedPhylumId	alignedClassName	alignedClassId	alignedOrderName	alignedOrderId	alignedFamilyName	alignedFamilyId	alignedGenusName	alignedGenusId	alignedSpeciesName	alignedSpeciesId	alignedPath	alignedPathIds	alignedPathNames
Fungi	NCBI:4751	Basidiomycota	NCBI:5204	Agaricomycetes	NCBI:155619	Agaricales	NCBI:5338	Agaricaceae	NCBI:5339	Agaricus	NCBI:5340	Agaricus bisporus	NCBI:5341	\| Eukaryota \| Opisthokonta \| Fungi \| Dikarya \| Basidiomycota \| Agaricomycotina \| Agaricomycetes \| Agaricomycetidae \| Agaricales \| Agaricineae \| Agaricaceae \| Agaricus \| Agaricus bisporus	NCBI:131567 \| NCBI:2759 \| NCBI:33154 \| NCBI:4751 \| NCBI:451864 \| NCBI:5204 \| NCBI:5302 \| NCBI:155619 \| NCBI:452333 \| NCBI:5338 \| NCBI:2982305 \| NCBI:5339 \| NCBI:5340 \| NCBI:5341	\| superkingdom \| clade \| kingdom \| subkingdom \| phylum \| subphylum \| class \| subclass \| order \| suborder \| family \| genus \| species
Fungi	OTT:352914	Basidiomycota	OTT:634628	Agaricomycetes	OTT:1012685	Agaricales	OTT:8364	Agaricaceae	OTT:8360	Agaricus	OTT:737448	Agaricus bisporus	OTT:564405	\| \| Eukaryota \| Opisthokonta \| Nucletmycea \| Fungi \| \| \| Dikarya \| Basidiomycota \| Agaricomycotina \| Agaricomycetes \| Agaricales \| Agaricaceae \| Agaricus \| Agaricus bisporus	OTT:805080 \| OTT:93302 \| OTT:304358 \| OTT:332573 \| OTT:5246132 \| OTT:352914 \| OTT:5576447 \| OTT:5584405 \| OTT:656316 \| OTT:634628 \| OTT:633300 \| OTT:1012685 \| OTT:8364 \| OTT:8360 \| OTT:737448 \| OTT:564405	no rank \| no rank \| domain \| no rank \| no rank \| kingdom \| no rank \| no rank \| subkingdom \| phylum \| subphylum \| class \| order \| family \| genus \| species
														Fungi \| Basidiomycota \| Agaricomycetes \| Agaricales \| Agaricaceae \| Agaricus bisporus		kingdom \| phylum \| class \| order \| family \
Fungi	IRMNG:14	Basidiomycota	IRMNG:236	Agaricomycetes	IRMNG:1108	Agaricales	IRMNG:10892	Agaricaceae	IRMNG:110489	Agaricus	IRMNG:1332778	Agaricus bisporus	IRMNG:11209605	Fungi \| Basidiomycota \| Agaricomycetes \| Agaricales \| Agaricaceae \| Agaricus \| Agaricus bisporus	IRMNG:14 \| IRMNG:236 \| IRMNG:1108 \| IRMNG:10892 \| IRMNG:110489 \| IRMNG:1332778 \| IRMNG:11209605	kingdom \| phylum \| class \| order \| family \| genus \| species
Fungi	GBIF:5	Basidiomycota	GBIF:34	Agaricomycetes	GBIF:186	Agaricales	GBIF:1499	Agaricaceae	GBIF:4170	Agaricus	GBIF:2518646	Agaricus bisporus	GBIF:5243447	Fungi \| Basidiomycota \| Agaricomycetes \| Agaricales \| Agaricaceae \| Agaricus \| Agaricus bisporus	GBIF:5 \| GBIF:34 \| GBIF:186 \| GBIF:1499 \| GBIF:4170 \| GBIF:2518646 \| GBIF:5243447	kingdom \| phylum \| class \| order \| family \| genus \| species
Fungi	GBIF:5	Basidiomycota	GBIF:34	Agaricomycetes	GBIF:186	Agaricales	GBIF:1499	Agaricaceae	GBIF:4170	Agaricus	GBIF:2518646	Agaricus bisporus	GBIF:5243447	Fungi \| Basidiomycota \| Agaricomycetes \| Agaricales \| Agaricaceae \| Agaricus \| Agaricus bisporus	GBIF:5 \| GBIF:34 \| GBIF:186 \| GBIF:1499 \| GBIF:4170 \| GBIF:2518646 \| GBIF:5243447	kingdom \| phylum \| class \| order \| family \| genus \| species

jhpoelen commented 1 year ago

For more context, see associated meeting notes at https://docs.google.com/document/d/1GKU6lc0BN3CFEbZ_VhSTnAOWfiQyjfYBvtUgU7PgfV0 .

ljwalker commented 1 year ago

Tested. It works! (As does running against WoRMS.)

jhpoelen commented 1 year ago

@ljwalker thanks for checking!

jhpoelen commented 1 year ago

@ljwalker I hope that Chrissy and Christina feel listened to, and looking forward to receiving more suggestions.

globalbioticinteractions / name-alignment-template

add separate columns for aligned taxon ranks and their ids #14