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Add more SO annotations to HGNC
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References #118
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cthoyt committed Nov 12, 2021
1 parent ad88c95 commit 5c778a3
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions src/pyobo/sources/hgnc.py
Original file line number Diff line number Diff line change
Expand Up @@ -101,9 +101,11 @@
LOCUS_TYPE_TO_SO = {
# protein-coding gene
"gene with protein product": "0001217",
"complex locus constituent": "0001217", # this is a nonsensical annotation for genes encoding complex members
"protocadherin": "", # TODO see https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/562
# non-coding RNA
"RNA, Y": "0002359",
"RNA, cluster": "", # TODO
"RNA, cluster": "", # TODO see https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/564
"RNA, long non-coding": "0002127", # HGNC links to wrong one
"RNA, micro": "0001265",
"RNA, misc": "0001266",
Expand All @@ -122,14 +124,12 @@
"pseudogene": "0000336",
# other
"T cell receptor gene": "0002133",
"complex locus constituent": "",
"endogenous retrovirus": "0000100",
"fragile site": "0002349",
"protocadherin": "", # TODO
"readthrough": "0000697", # maybe not right
"region": "",
"transposable element": "0000111", # HGNC links to wrong one
"virus integration site": "", # TODO
"virus integration site": "", # TODO see https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/551
"region": "0001411", # a small bucket for things that need a better annotation, even higher than "gene"
"unknown": "0000704", # gene
None: "0000704", # gene
}
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