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Fix the open parser issues #209 to #225 - #226

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fix/open-issues-209-225
Nov 1, 2026
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mdoering merged 14 commits into
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fix/open-issues-209-225

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Fixes every open issue except #30 (help wanted). One commit per issue, or per group where the issues share a fix.

Read together, the issues overlapped in five groups: separators and blacklists (#209, #210, #211), notes in the authorship (#217, #220, #222), author tokens (#213, #218, #219, #221), qualifiers and ranks (#214, #215), and alternatives (#212, #225, plus the pipe from #219).

Changes

Issue Before After
#225, #212 Festuca rubra/arenaria: species with author arenaria INFORMAL, genus Festuca, phrase rubra/arenaria, state partial
#225 Bombus terrestris or lucorum: trinomial the same, phrase terrestris or lucorum
#212 Uria aalge/Alca torda, Anser/Branta: first name with an author unparsable OTHER
#210 Apidae-223957883: unparsable uninomial Apidae, phrase 223957883
#209 Sus_spec_2, Acrocirridae_gen1: unparsable genus Sus, phrase spec_2; uninomial Acrocirridae, phrase gen1
#211 Genus sp., ADN Suelo, Wurm-8005097 unparsable; five new blacklisted epithets
#213 Priscula Dup9, Actia Janzen05: code as author phrase; (Linnaeus1758) splits off the year; new warning for an author still holding a digit
#214 Canis lupus familiaris cf.: quadrinomial qualifier on the last epithet; also (cf.) and Engl. cf. var. giganteum
#215 DC. subp. japonica: unparsed subspecies
#216 (BIN BOLD:ADH3884): basionym author BIN Bold phrase BOLD:ADH3884
#217 L.s.l., Øvst.ined: one author author and note
#218 vanAchterberg, (deGeer, 1778): epithet, unparsed authors van Achterberg, de Geer
#219 Singer | M.M. Moser: one author two authors
#220 W.J. Kress, sp. nov., ined. 2013: author sp. note sp. nov. ined., year 2013
#221 Rech. fil. subsp. bourgeaui: unparsed subspecies
#222 Fisher & Orth, 1978: note Orth. authors Fisher, Orth

Decisions to check

Left as they are

  • A slash right after the genus with a lower-case word behind it: Belaustium/microsmaris, Hypsithocus / hynsithocus Bergroth, 1927.
  • Alternatives with authors or rank markers in the first name: Sorbus udvardyana Somlyay et Sennikov / S. pelsoensis Németh, Viola curtisii ssp. coniophila|Viola tricolor.
  • Sus_spec_2 renders as Sus sp. spec_2 in name-parser-api's own NameFormatter, which has a separate copy of the phrase marker. No ChecklistBank name has this shape.

Impact

  • ChecklistBank verbatim names, on candidate sets of about 650,000 rows picked by the shapes above: 15,385 distinct names change. About 2,280 become informal alternatives, about 330 become unparsable alternatives, and about 7,260 carry the new warning.
  • COL XR 26.6, all 6.4M names: 954 rows change, all reviewed by group. 787 Anon.ined. (now an anonymous author with the note), 85 glued particles, 49 Orth, 19 with the new warning, 10 Genus … and 4 others.
  • The candidate sets are shape-based, so changes outside those shapes in ChecklistBank were not measured. The COL XR comparison covers all of its names.

"Festuca rubra/arenaria" and "Bombus terrestris or lucorum" name no one
species: the identification stopped at several. The second epithet was
read as a combination author, or the "or" dropped, so name matching took
the first species as the identification. With one genus the name is now
INFORMAL, anchored on that genus (and subgenus), the rest its phrase,
left partial. A qualifier may stand before the epithet ("Agabus cf.
lutosus/griseipennis"). A rank hint changes nothing; a separate authorship
joins the phrase, as on any informal name without an epithet.

With two genera there is no one taxon to claim: "Uria aalge/Alca torda",
"Anser/Branta" and "Zea mays/Aspergillus flavus mixed library" are
unparsable OTHER. "Larus marinus or Larus hyboreus" in one genus moves
from OTHER to informal. A capital alone may be an author ("Festuca
rubra/Hackel"), a strain code is no epithet, a hybrid formula stays one,
and "Tethea or hibernica" keeps the moth's epithet "or".

ChecklistBank verbatim names: about 2,280 distinct names become informal,
about 330 unparsable.

Closes #225
Closes #212
"Apidae-223957883" and "Acrocirridae_gen1" were rejected as junk, like any
single word with a digit, although "Apidae 223957883" parses. A capitalised
word, a dash and a number, or an underscore and a lower-case label with a
digit, is now that taxon with the label as its phrase. So is the first word
of "Abies_01 sp_01" and "Strat_genus3 sp. 1", whose genus held the label.

An underscored indet marker stands for the space: "Sus_spec_2" reads as
"Sus spec_2", and "spec_2" joins "sp_2" as an indet designation instead of a
species epithet. "Entodinium_1" and "Oxalis_barrelieri" are unchanged, as is
a virus ("Crucivirus-112").

Closes #209
Closes #210
The first word of "ADN Suelo" and "Wurm-8005097" and a herbarium record
("HNT_Specimen:5625_Accession:29540") are no name, OTHER. The word "Genus"
before anything else ("Genus sp.", "Genus B sp. 1") and "unpublished name"
are placeholders.

"accession", "parasite", "sample", "specimen" and "western" join the epithet
blacklist, and flag a name doubtful. "Stomoxys parasite Fabricius, 1781" and
"Halodactyle parasite Van Beneden, 1845" are real and go on the whitelist.

Closes #211
"Fisher & Orth, 1978" lost its second author to a nomenclatural note "Orth.",
as the note's abbreviation is matched in any case, with or without its dot.
"Orth" with no dot and no lower-case word behind it is a surname now. "Orth. var."
stays a note, and so does a capitalised "Nomen". About 100 distinct ChecklistBank
names, mostly American dipterists.

Closes #222
In "Heliconia waoraniana W.J. Kress, sp. nov. ined. 2013" the "sp." became an
author and "nov. 2013" was left unparsed, as the note was only recognised at the
end of the string or before certain words. "ined." may now follow it after a
comma, and the year may follow any note without one. The year goes to the
authorship, the note stays "sp. nov. ined.".

Closes #220
"Arenaria ciliata L.s.l." and "Placynthium pulvinatum Øvst.ined" had one author
"L.s.l." and "Øvst.ined". A sensu note (s.l., s.str., s.s., s.lat., s.ampl.),
"ined" or "auct" right after the dot of a capitalised abbreviation now stands as
if a space were there, on the name string and in a separate authorship.

Closes #217
"Aphidius tarsalis vanAchterberg 2006" had the infraspecific epithet
"vanAchterberg", and "(deGeer, 1778)" stayed unparsed. A lower-case van, von, de,
der, den, del, du, di, da, la or le right before a capitalised surname stands as
if a space were there, on the name string and in a separate authorship. About 460
distinct ChecklistBank names, mostly deLoriol, deMeijere, deGeer and duPont. A
capital belongs to the surname: LeConte.

Closes #218
"Panaeolus cyanescens (Berk. | Broome) Sacc." and "Macrolepiota olivascens Singer
| M.M. Moser" read the two authors as one. A pipe between two capitalised words,
past the genus, is now an ampersand, on the name string and in a separate
authorship. Elsewhere it stays a word break: "Rosa rubiginosa| L. s.l.".

A pipe between epithets or names reads as the slash does: "Salicornia
pusilla|Salicornia disarticulata" keeps only the genus, "Abramis brama|Blicca
bjoerkna" and "Bilderdykia|Polygonum" are unparsable.

Closes #219
"Allium bourgeaui Rech. fil. subsp. bourgeaui" left the subspecies unparsed, as
only "f." was known to continue a species author before a rank marker.

Closes #221
"Priscula Dup9", "Actia Janzen05" and "Priscula Ven02/80-085" had a code for an
author, as had "Agrobacterium pusense L2/2/1": about 3,500 and 1,500 distinct
ChecklistBank names. A capitalised word with a digit, all that follows a
uninomial, is its phrase now, and a code after a binomial may hold a slash and
follow a genus in square brackets, as in "[Eubacterium] rectale M104/1".

A year glued to its author is split off: "(Linnaeus1758)", "Totton1930".

Any author that still holds a digit gets the new warning "author with attached
number".

Closes #213
"Aegialites debilis (BIN BOLD:ADH3884)" had the basionym author "BIN Bold". A
BOLD BIN or SH code after a name may stand in brackets now, with or without its
BIN label, and goes to the phrase as it does without them.

Closes #216
… too

"Youngia japonica (L.) DC. subp. japonica" left the subspecies unparsed. Of the
markers one letter off, only "subsp" has all its letters, and a dropped letter is
the usual slip. A misspelt marker is now also repaired after a species author,
not only between two epithets.

Closes #215
"Canis lupus familiaris cf." had "cf" for an epithet of a quadrinomial, "Amanita
gilbertii Beauseign. cf." an author "Beauseign.cf.", and "Protium giganteum Engl.
cf. var. giganteum" lost the variety to it. A cf., aff. or nr. trailing a name
with more than a species epithet, in a bracket at the end ("(cf.)"), or between
the species author and an infraspecific epithet is now the epithet qualifier of
the name's last epithet, on the name string and in a separate authorship. After
the author only with a rank marker or as an autonym: others are mostly second
names ("Septifer bilocularis Brachidontes cf. variabilis").

A bare qualifier on a genus ("Ulnaria cf.") stays the phrase of an unnamed species,
like "sp.".

Closes #214
@mdoering
mdoering merged commit 2647781 into main Nov 1, 2026
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@mdoering
mdoering deleted the fix/open-issues-209-225 branch November 2, 2026 00:04
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