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Metadata ingest for biosamples in GOLD - study Gs0154044 #42

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aclum opened this issue Jan 19, 2023 · 11 comments · Fixed by microbiomedata/sample-annotator#113
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@ssarrafan
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@ssarrafan ssarrafan changed the title ingest GOLD study Gs0154044 Metadata ingest for biosamples in GOLD - study Gs0154044 Jan 20, 2023
@turbomam
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This issue does not belong in the nmdc-schema repo because it does not request changes to the schema. It might make sense to put it in sample-annotator.

@turbomam turbomam transferred this issue from microbiomedata/nmdc-schema Jan 23, 2023
@turbomam
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HI @aclum @ssarrafan @sujaypatil96

This (and it's sub-issues) are important valid, but they don't belong in the nmdc-schema repo. I have moved all of them to the issues repo.

@aclum aclum assigned aclum and unassigned sujaypatil96 Jan 24, 2023
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aclum commented Jan 24, 2023

Capturing the extra soil metadata depends on GOLD ticket https://issues.jgi.doe.gov/browse/GOLD-2048
I've asked Reddy via email to update the envo triad for the root endosphere samples. After considering using some PO terms, with Montana's approval we went with some existing envo terms.
local environmental context ENVO_01001057 'environment associated with a plant part or small plant'
environmental medium of [ENVO_01000349]](http://purl.obolibrary.org/obo/ENVO_01000349) 'root matter'

@aclum aclum added the GSP Label to indicate work is needed to meet GSP 2023 goals label Jan 26, 2023
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aclum commented Jan 27, 2023

Depends on microbiomedata/sample-annotator#113

@aclum aclum removed their assignment Jan 27, 2023
@ssarrafan ssarrafan moved this to 📋 Backlog in GSP 2023 Board Jan 27, 2023
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aclum commented Jan 31, 2023

Asked Reddy for an update on https://issues.jgi.doe.gov/browse/GOLD-2048

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aclum commented Jan 31, 2023

ETA on GOLD-2048 is Friday or Monday (2/6/23)

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aclum commented Jan 31, 2023

Depends on schema changes to support tax id for host microbiomedata/nmdc-schema#699

Based on the squad meeting discussion @sujaypatil96 will make the following updates

  • collected_from to be populated with an id of class FieldResearchSite
  • parse the suffix after '-' in biosampleName and use that to populate the samp_name slot for the biosamples
  • [Add biogeochemical data for soil samples ](https://github.com/microbiomedata/sample-annotator/issues/115)

@sujaypatil96
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sujaypatil96 commented Feb 3, 2023

The code in the linked PR is already capable of handling points 1 and 2. Point 3 is on hold.

@ssarrafan ssarrafan moved this from 📋 Backlog to 🏗 In progress in GSP 2023 Board Feb 3, 2023
@aclum
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aclum commented Feb 3, 2023

The soil measurements do not uniquely map to sample names and this requirement will be dropped for now.

@sujaypatil96 sujaypatil96 moved this from 🏗 In progress to 🔖 Ready in Bioscales Squad Board Feb 7, 2023
@aclum aclum moved this from 🔖 Ready to 🏗 In progress in Bioscales Squad Board Feb 8, 2023
@sujaypatil96 sujaypatil96 moved this from 🏗 In progress to 🔖 Ready in Bioscales Squad Board Feb 9, 2023
@aclum aclum moved this from 🔖 Ready to 👀 In review in Bioscales Squad Board Feb 10, 2023
@ssarrafan
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This looks like it's still in progress so I'll move to the new sprint.

@ssarrafan ssarrafan moved this from 🏗 In progress to 👀 In review in GSP 2023 Board Feb 25, 2023
@github-project-automation github-project-automation bot moved this from 👀 In review to ✅ Done in Bioscales Squad Board Mar 14, 2023
@github-project-automation github-project-automation bot moved this from 👀 In review to ✅ Done in GSP 2023 Board Mar 14, 2023
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