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NCBI Ingest: Correct geolocation metadata mappings #2788

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anna-parker opened this issue Sep 15, 2024 · 1 comment
Open
1 of 3 tasks

NCBI Ingest: Correct geolocation metadata mappings #2788

anna-parker opened this issue Sep 15, 2024 · 1 comment
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bug Something isn't working epic A major task that should be broken down into smaller tasks ingest Ingest pipeline

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@anna-parker
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anna-parker commented Sep 15, 2024 •
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  • Curate NCBI geolocation metadata #3105
    image

  • Additionally we map ncbiGeoRegion we map to geoLocAdmin2, which is not correct as ncbiGeoRegion corresponds to continent and geoLocAdmin2 should be "A local administrative region from which the sample was collected (ex: county or municipality)":
    image

  • Can we reconsider the displayName for these fields? I think it will be confusing to submitters that geoLocAdmin1 gets mapped to collection subdivision etc.
@anna-parker anna-parker added the bug Something isn't working label Sep 15, 2024
@chaoran-chen chaoran-chen added the ingest Ingest pipeline label Sep 15, 2024
@corneliusroemer
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Yeah this was on my list of things to fix/improve eventually. Thanks for making an issue.

@anna-parker anna-parker mentioned this issue Sep 15, 2024
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@corneliusroemer corneliusroemer mentioned this issue Sep 18, 2024
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corneliusroemer added a commit that referenced this issue Sep 18, 2024
@corneliusroemer
fix: don't ingest region as geoLocAdmin2 (it's continent)
ab8fac9 
Relates to #2788

Might require pp values.yaml changes - need to check
@corneliusroemer corneliusroemer mentioned this issue Sep 18, 2024
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corneliusroemer added a commit that referenced this issue Sep 18, 2024
@corneliusroemer
fix: don't ingest region as geoLocAdmin2 (it's continent)
7c0a0ca 
Relates to #2788

Might require pp values.yaml changes - need to check
corneliusroemer added a commit that referenced this issue Sep 18, 2024
@corneliusroemer
fix: don't ingest region as geoLocAdmin2 (it's continent) (#2833)
5c0b84e 
Relates to #2788

Might require pp values.yaml changes - need to check
@anna-parker anna-parker added the epic A major task that should be broken down into smaller tasks label Oct 29, 2024
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@chaoran-chen @corneliusroemer @anna-parker