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new voting sheets, generated in Python (notebook) not Makefile #270

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new voting sheets, generated in Python (notebook) not Makefile #270

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@turbomam turbomam commented Nov 14, 2024 •
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needs better documentation/organization/refresh plans for the files currently in notebooks/environmental_context_value_sets/

mam-env-package-overrides.tsv: can't be recreated from within this repo. do not delete.

common.py: nobody uses this yet. there are some functions that use global dicts for very crude caching

pulled on demand, not committed:

  • ncbi_biosamples_2024-09-23.duckdb
  • ncbi_biosamples_2024-09-23.duckdb.gz
  • goldterms.db
  • goldterms.db.gz
  • ncbi_biosamples_2024-09-23_package_usage.tsv
  • nmdc_env_package_predictions.tsv
  • environmental_context_value_sets.Makefile
  • environmental_context_value_sets/README.md

@turbomam turbomam linked an issue Nov 14, 2024 that may be closed by this pull request
quick prototype of voting sheet generation in notebook in this repo #268
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@turbomam turbomam changed the title recapitulate soil env_broad_scale voting sheet in Python (notebook) not Makefile recapitulate voting sheet generation in Python (notebook) not Makefile Nov 15, 2024
@turbomam turbomam changed the title recapitulate voting sheet generation in Python (notebook) not Makefile new voting sheets, generated in Python (notebook) not Makefile Nov 22, 2024
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turbomam commented Nov 22, 2024 •
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Here are the PO terms that were used by any of our sources for plant-associated env_medium::

it appears that they are all present in EnvO too

PO:0000003,whole plant
PO:0009007,portion of plant tissue
PO:0009008,plant organ
PO:0009011,plant structure
PO:0025025,root system
PO:0025034,leaf

If they have a common root, maybe we should include more terms from that hierarchy?

I guess the current envo_native column in the voting sheets doesn't do a good job of distinguishing EnvO native terms, terms imported into EnvO from other sources, and CURIes that use the ENVO prefix but don't really denote any EnvO class.

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turbomam commented Nov 22, 2024 •
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Here's their is_a tree

plant-associated-biosample-env-medium-po-terms-is_a-to-mat-ent

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We could add more of these plant structure descendants without needing to consult any additional ontologies

plant-structures-in-envo

@turbomam turbomam marked this pull request as ready for review December 6, 2024 22:30
@turbomam turbomam requested a review from cmungall December 6, 2024 22:30
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closing in favor of

@turbomam turbomam closed this Dec 17, 2024
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quick prototype of voting sheet generation in notebook in this repo
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