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Build # 33190598935

Build Type

push

github

Committed by web-flow

Commit Message

Curate the published water buffalo loci (#121)

Checking whether Bubalus bubalis belongs under Bos sp. (#109, #115 --
it does, the tree is prefix scope) turned up a real gap: the entry did
not record the loci the buffalo papers actually characterize. It
declared DQA, DQA1 and DQB, and inherited everything else from cattle.

Declared DRA, DRB and DQA2 as well. Sources cited on the entry:

  PMID 12580780  buffalo DRA and DRB, eight Bubu-DRB alleles
  PMID 22383896  cites isolation of buffalo DQA1 and DQA2 cDNAs
  IPD-MHC        39 Bubu-DQA alleles

Bubu-DRB no longer renames to Bubu-DRB3. gene_aliases.yaml maps
DRB -> DRB3 under BoLA, which is correct for cattle, where DRB3 is the
expressed DRB locus, and buffalo inherited it. PMID 22383896 says only
that "the Bubu-DRB sequence showed maximum homology with the
BoLA-DRB3*0101 allele of cattle" -- homology, not identity -- and every
paper writes the buffalo locus as Bubu-DRB. Declaring DRB on the species
stops the rename. Bubu-DRB3 still parses by inheritance, and BoLA-DRB
still resolves to DRB3 for cattle.

BoLA-DQB3 and BoLA-DQB4 are deliberately NOT added. A trans-species
phylogeny paper assigns buffalo sequences to loci it labels BoLA-DQB1,
BoLA-DQB3 and BoLA-DQB4, but IPD-MHC registers only BoLA-DQB, so those
are that analysis's locus labels rather than designations. A test pins
their absence.

No change on real data: 0 of 11,558 names in the bundled corpora parse
differently.

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

Coverage Stats

4073 of 4574 relevant lines covered (89.05%)

0.89 hits per line