app/data/organisms.ts

Functions

Imports

It imports no other module of this repo. Imported by app/lib/cv/markdown.mjs, app/lib/publications/exports.mjs, app/lib/scientific-names.tsx.

Source

1/**
2 * Organism names to italicize in publication titles and abstracts. A reviewed allowlist, not a
3 * pattern: a "Capitalized lowercase" match would italicize Rio Grande and ordinary sentence openings.
4 * Longest first, because the matcher takes the first alternative that fits and would otherwise leave
5 * a subspecies epithet upright. Virus agent names and phage isolate names are left out on purpose:
6 * they are not formal taxa.
7 */
8
9const ORGANISMS: readonly string[] = [
10  "Meleagris gallopavo intermedia",
11  "Meleagris gallopavo silvestris",
12  "Tympanuchus cupido attwateri",
13  "Arthrobacter globiformis",
14  "Microbacterium foliorum",
15  "Mycobacterium smegmatis",
16  "Meleagris gallopavo",
17  "Tympanuchus cupido",
18  "Cairina moschata",
19  "Gallus gallus",
20  // Bare genus: only Mycobacterium occurs unbound in the corpus.
21  "Mycobacterium",
22];
23
24/**
25 * Every listed name as one global pattern, whole words only. ORGANISMS is ordered longest first and
26 * alternation takes the first branch that matches, so the trinomial wins over the binomial. Global,
27 * so read it with `matchAll` or `replace`, which do not leave `lastIndex` behind.
28 */
29export const ORGANISM_PATTERN = new RegExp(
30  `\\b(${ORGANISMS.map((name) => name.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")).join("|")})\\b`,
31  "g",
32);