nmdc-schema

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Factor `TextValue` out of nmdc-schema and migrate accordingly

3

see also - #1224 [AttributeValue](https://microbiomedata.github.io/nmdc-schema/AttributeValue/)s provide structure for values that MIxS models (and NCBI stores) as strings [TextValue](https://microbiomedata.github.io/nmdc-schema/TextValue/) is a wrapper around `string` that theoretically adds value by specifying the...

turbomam

change nmdc-schema's MIxS import to GSC's 6.2 YAML

18

currently slightly ahead of MIxS 6.0: https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml change to: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml see also - https://github.com/microbiomedata/nmdc-schema/issues/299

turbomam

This is Yuri's code for re-iding. Review should focus on nmdc_schema/metab_id_refactor.py as other files python files were not used, instead Michael refactored them into code in nmdc_automation repo.

aclum

Create declarative mapping file for NCBI BioSample ingest

7

A big data source that we will be ingesting multiple studies from in the coming weeks/months is NCBI, and for this we need a generic NCBI study/BioProject to NMDC ingest...

sujaypatil96

report mixs package/term association counts from sheets-for-nmdc-submission-schema

1

https://docs.google.com/spreadsheets/d/1cMlPKgjZh-v21aMYCm9x1TxzE5BwGQptBQcvuaYAtC8/edit#gid=1742830620

turbomam

Submission Portal- soil template -horizon

3

The slot 'horizon' & 'horizon method' are commented out of the Biosample class slots list in nmdc.yaml. Why? Both still appear on the submission portal. horizon is also commented out...

mslarae13

support validation of nmdc-schema data objects against stricter submission-schema rules

1

currently requires flattening nmdc-schema data objects to match the tabular orientation of the submission schema possible solution: add environment-specific Biosample subclasses to nmdc-schema

turbomam

That would facilitate the addition of doctests to the migrator in https://github.com/microbiomedata/berkeley-schema-fy24/pull/127.

eecavanna

migrator for berkeley schema slot has_calibration

5

Just a noting that in nmdc-schema has_calibration has a range of a string and is currently populated with either a data object identifier, "False", or "false". In the berkeley schema...

aclum

Currently the `principal_investigator` slot is single valued, but some consortia have multiple principal investigators like WHONDRS and EMS. They have multiple people listed as a single value string (with a...

brynnz22