bcgsc / pori_graphkb_loader

The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API
https://bcgsc.github.io/pori
GNU General Public License v3.0
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Support new Fusion notation recommendations #76

Closed creisle closed 2 years ago

creisle commented 2 years ago

A new recommendation on the formatting of fusions was released which has formalised use of the :: for notating/separating fusion genes. In the long term we should move this notation to the parser, in the short term we will need to update the civic fusion parser here a they have begun updating entries already

creisle commented 2 years ago

This will resolve the loader errors which currently look like this (the variant parser falls back to looking for a named term on failure to parse)

2022-03-11T18:50:28.843Z error: evidence (8509) Error: missing Vocabulary record where {"AND":[{"sourceId":"bcr::abl f317l"},{"source":{"filters":{"name":"graphkb"},"target":"Source"}}]}
cgrisdale commented 2 years ago

HUGO gene nomenclature committee (HGNC) recently published recommendations on gene fusion naming including the change to a '::' delimiter between fusion partner genes. https://www.nature.com/articles/s41375-021-01436-6