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Mixed up division/location fields for US #10

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joverlee521 opened this issue Aug 14, 2024 · 0 comments
Open

Mixed up division/location fields for US #10

joverlee521 opened this issue Aug 14, 2024 · 0 comments
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@joverlee521
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joverlee521 commented Aug 14, 2024

Noticed during 1:1 w/ @kimandrews that USA records have a mix of state and counties in the division and location fields.

Small subset of examples
accession accession_version strain date region country division location
AF394868 AF394868.1 1265 North America USA Monterey California
AF394869 AF394869.1 2253 North America USA California
AF394870 AF394870.1 3044 North America USA Arizona
AF394871 AF394871.1 1566 North America USA Plumas County California
AF394872 AF394872.1 2847 North America USA Lewis County Washington

Looking at GenBank record for one of the examples (AF394868), the geo_loc_name is "USA: Monterey, California".

This does not follow the pattern for GenBank's geo_loc_name (<country_value>[:<region>][, <locality>]) that we expect in augur curate parse-genbank-location.

Possible solutions

  1. Add geolocation rules to correct these records for rabies
  2. Programmatically catch these mix ups in augur curate parse-genbank-location (parse-genbank-location should warn about region/locality mix ups augur#1578)
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