pirl-unc / mhcgnomes / 33534855184
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coverage: 89.656% (+0.02%) from 89.635%
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Curate the low-resolution (Lr-) swine haplotype series (#162) (#183)

I had twice reported this data as paywalled: PMC has no full text for Ho et al.
2009 or Hammer et al. 2020, and the cohort papers' PMC HTML carries only
per-line counts. What I never tried was Europe PMC, which serves the same
articles as structured full-text XML. Tables 1 and 2 of PMC8362188 are in it
complete, 49 class I and 31 class II rows. My greps for "Lr-" had also been
missing them because the XML uses a Unicode hyphen.

59 haplotypes curated, 39 class I and 20 class II. Every member is a one-field
allele, because that is what a group specificity is: 1*04 is SLA-1*04XX, any
allele in group 04.

The footnotes carry the important part. Table 1's footnote 5 reads "Untyped SLA
class I locus", and Lr-24.0 and Lr-33.0 show Blank *with that footnote* -- the
same word as Lr-23.0's plain Blank, and the opposite claim. Importing the table
without reading its footnotes would have recorded two untyped loci as
positively absent, which is precisely the distinction #162 was filed about.

19 rows are deliberately left out with their reasons recorded in the YAML and
pinned in a test: composite or unconfirmed names, untyped loci, "+" meaning an
allele beyond the group, and "/" meaning alternatives at one locus. The last
two need a disjunction member, the only part of #162 still open.

Unlooked-for cross-validation: footnote 3 says Lr-02.0 "did not appear to
possess an expressed SLA-3 gene", the same fact Table 2 of PMC5472656 records
as Hp-2.0's SLA-3 being null. Two papers, one haplotype at two resolutions.

0 of 36,752 corpus names change; 0 printed forms fail to parse back.

Claude-Session: https://claude.ai/code/session_012s4siLj2Vm33eNMGjNSazH

4325 of 4824 relevant lines covered (89.66%)

0.9 hits per line

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