name2taxid includes some questionable material

[arendsee]

This happens:

> name2taxid("s2")
"164330"
 > name2taxid("s2") %>% taxid2name
"Thauera aminoaromatica"

S2 is a strain name for this bacteria. See here.

The problem is that I allow matches against any name_class. Here are all the name classes in the database:

name_class	count(name_class)
acronym	1167
anamorph	302
authority	410075
blast name	229
common name	14204
equivalent name	25058
genbank acronym	486
genbank anamorph	107
genbank common name	28182
genbank synonym	2958
in-part	628
includes	36595
misnomer	1386
misspelling	35975
scientific name	1689025
synonym	168033
teleomorph	179
type material	11449

So the question is, which of these should we include?

Most of them seem pretty reasonable. The problematic ones are type material and acronym. Perhaps we should allow the user to select which name classes to allow?

[sckott]

Perhaps we should allow the user to select which name classes to allow?

that seems reasonable, by default excluding type material and acronym?

[arendsee]

@sckott Sounds good. Is this an issue in taxize as well?

[sckott]

this is what we get with get_uid

taxize::get_uid("s2")
#> 
#> Retrieving data for taxon 's2'
#> 
#> [1] "164330"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.ncbi.nlm.nih.gov/taxonomy/164330"

[maelle]

unarchiving it thanks to @stitam 😸