catalog resources that contain all or a subset of MIxS terms

[turbomam]

Google sheets:

• MIxS 6 term updates/MIxS6 packages - Final_clean
• MIxS 6 term updates/MIxS6 Core- Final_clean
• Could these have been accidentally or maliciously modified? what's an upstream source of truth?

  Some frozen Excel representation of the Google Sheets?

• Chris Hunter recommended https://github.com/GenomicsStandardsConsortium/mixs/tree/main/mixs/excel

GSC's mixs.yaml

• used @cmungall's mixs_converter.py to convert the Google Sheets

Various incarnations of NMDC's mixs.yaml

• ~2023-02-15, https://github.com/microbiomedata/nmdc-schema/commit/3824b9f2ecbd165a4b0fa6387d0faad508eaf772: converted from Google sheets with the sheets_and_friends package, based on branch https://github.com/microbiomedata/sheets_and_friends/tree/issue-163-mixs-subsetter
  • see src/schema/mixs.yaml target
  • does a lot of modification with Mike Farah's GO-base yq
• ~2022-04-26, https://github.com/microbiomedata/nmdc-schema/commit/7751c0b37cc67c1e95d8f1e42afd052fb2838bb3
  • created by rebuild_mixs_yaml.py
  • used some input with a name like _slotroster.tsv, which may have been created by _slotroster.py
  • considered many factors when deciding which terms to include in mixs.yaml
  • slots used by documents in mongodb's biosample_set collection
  • slots claimed by the Biosample class in nmdc.yaml
  • slots already defined in the mixs.yaml from previous commits
  • slots used in the DataHarmonizer interface defined by sheets_and_friends
• ~ 2021-08-31 https://github.com/microbiomedata/nmdc-schema/commit/d8c1b69cce92b5b9ca494d4bf8fde3f0d6b5f1fc
  • first created 2021-04-02 :gift: https://github.com/microbiomedata/nmdc-schema/commit/94a30698f41357254f139c61b130b76922bc55bd with mixs6.py from microbiomedata/metadata_converter?
  • some additional refinements after 2021-08-31

nmdc_submission_schema.yaml

• created by https://github.com/microbiomedata/sheets_and_friends, using various incarnations/variants of sheets-for-nmdc-submission-schema, esp. the import_slots_regardless and modifications_long tabs.
• As of ~2023-02-15, import_slots_regardless imports MIxS terms from NMDC's mixs.yaml file. Previously they were imported directly from GSC's mixs.yaml
• modifications_long could be seen as "in conflict with" the yq modification in NMDC's current mixs.yaml pipeline
• the same could have been be said for the manually entered slot_usages on Biosample in nmdc.yaml, although those have been propagated into modifications_long on most recent sheets-for-nmdc-submission-schema variants

[turbomam]

Additional content or issues in

• https://github.com/microbiomedata/archived-metadata-notebooks

• https://github.com/microbiomedata/attributes-of-biosamples

• https://github.com/microbiomedata/cleanroom-schema

• https://github.com/microbiomedata/DataHarmonizer

• https://github.com/microbiomedata/dh_testing

• https://github.com/microbiomedata/GOLD-ontology-translation

• https://github.com/microbiomedata/iot_to_linkml

• https://github.com/microbiomedata/metadata_converter

• https://github.com/microbiomedata/mixs

• https://github.com/microbiomedata/MIxS-ontology-translation

• https://github.com/microbiomedata/mixs_fresh_start

• https://github.com/microbiomedata/nmdc-metadata

• https://github.com/microbiomedata/nmdc-ontology

• https://github.com/microbiomedata/NMDC_Planning ?

• https://github.com/microbiomedata/nmdc-schema

• https://github.com/microbiomedata/sample-annotator

• https://github.com/microbiomedata/schema_hackathon

• https://github.com/microbiomedata/sheets_and_friends

• https://github.com/microbiomedata/use-nmdc-schema

• https://github.com/turbomam/badexperiment

• https://github.com/turbomam/DataHarmonizer ?

• https://github.com/turbomam/envo-robot-helpers

• https://github.com/turbomam/hident

• https://github.com/turbomam/mixs-source ?

• https://github.com/turbomam/nmdc-mixs-supplement-for-envo

• https://github.com/turbomam/sample-annotator

• https://github.com/turbomam/scoped-mapping

https://github.com/microbiomedata/issues