pirl-unc / mhcgnomes / 33476439053
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coverage: 89.417%. Remained the same
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Finish the IPD-MHC namespace sweep; establish 15 more prefixes (#131) (#165)

ipd_designations.yaml covered eight of the eleven IPD-MHC groups; the header
said NHP, FISH and CHICKEN were "the tail of #131". Transcribed them, plus the
Bos sp. group row, taking the file from 55 rows to 125. The eight groups
already there were re-read at the same time and every row still agreed.

The completed sweep finds zero disagreements: all 125 designations match our
prefix and every species IPD lists is in the ontology. CI now checks the whole
published namespace instead of two thirds of it.

Three groups are much smaller than they look, which is the useful part. FISH is
two species, CHICKEN is one, and there is no Bos taurus row at all -- cattle
are filed as "Bos sp. (BoLA)". So Bota is literature usage rather than a
committee assignment, and every other fish and bird here has a generated prefix
or a citation.

Fifteen prefixes established, 130 -> 146 designated: Gaga, Onmy and Sasa from
IPD, and Bota, Feca, Cyca, Coja, Saha, Xela, Modo, Anda, Dare, Ptal, Satr plus
H2 read verbatim from the papers.

Iibi is not a species prefix. Greater prairie chicken carried it with the note
"mhcseqs uses Iibi -- unusual but attested"; nothing attested it. PubMed has no
occurrence and the nucleotide database has exactly one, GenBank JX971120.1,
where IIBI is a gene symbol annotated /product="MHC class II antigen beta chain
2". Tycu meanwhile names 80 GenBank records at allele level (Tycu-BLB*26 and
siblings) and is the Klein two-plus-two code for the binomial. Tycu is now the
prefix; Iibi is kept as an other prefix so strings already emitted under it
still parse, but nothing is written with it.

The IPD NHP table also gives a second authority on the six primate _LA codes:
66 primates listed, every one with a two-plus-two code, none of them ChLA,
GoLA, MaLA, OmLA, OrLA or RhLA.

Thirty entries remain unestablished and are left alone.

40 of 36,752 corpus names change, every one t... (continued)

4250 of 4753 relevant lines covered (89.42%)

0.89 hits per line

Jobs
ID Job ID Ran Files Coverage
1 33476439053.1 41
89.42
 GitHub Action Run
Source Files on build 33476439053