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Fixup: Add date annotations for rare genotypes #38

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Fixup: Add date annotations for rare genotypes #38

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24 changes: 24 additions & 0 deletions ingest/defaults/annotations.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ AF266286 genotype_ncbi A
# WHO genotype reference strains
# Information from https://www.who.int/publications/i/item/WER8709
# Dates are retrieved from epi-weeks reported within strain names
# Dates are defined as the first day of the epi-week
AF045212 is_reference TRUE
AF045217 is_reference TRUE
AF079555 is_reference TRUE
Expand Down Expand Up @@ -146,3 +147,26 @@ U64582 date 1988-XX-XX
X84865 date 1994-XX-XX
X84872 date 1990-XX-XX
X84879 date 1971-XX-XX
#
# Strains with rare genotypes
# Dates are retrieved from epi-weeks reported within strain names on NCBI
# Dates are defined as the first day of the epi-week
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non-blocking

"first day" is somewhat ambiguous — could be Sunday, could be Monday… Better be explicit.

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# Dates are defined as the first day of the epi-week
# Dates are defined as the Monday of the epi-week

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I agree this needs to be more explicit. There are many different definitions for epi-weeks, and so the most precise wording for what I did would be "Dates are defined as the first day of the ISO epi-week, which is always a Monday". I can add this info to the annotations.tsv file. It also may be worth discussing whether there is a better approach for defining dates from epi-weeks reported in measles strain names. I started a discussion about this in slack.

# These are force-included in the nextclade tree to boost representation of rare genotypes
AF410989 genotype_ncbi E
AY037009 genotype_ncbi G2
AY037043 genotype_ncbi H2
AY037026 genotype_ncbi H2
AY037028 genotype_ncbi D2
FJ668380 genotype_ncbi D10
AF410989 strain MVi/Montreal.CAN/11.87
AY037009 strain MVs/California.USA/24.00[G2]
AY037043 strain MVi/Alaska.USA/16.00[H2]
AY037026 strain MVi/Minnesota.USA/13.97[H2]
AY037028 strain MVi/New York.USA/11.00[D2]
FJ668380 strain MVi/London.GBR/7.03[D10]
AF410989 date 1987-03-09
AY037009 date 2000-06-12
AY037043 date 2000-04-17
AY037026 date 1997-03-24
AY037028 date 2000-03-13
FJ668380 date 2003-02-10