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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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NMDC schema slots to NCBI MIxS term matching #1946

Closed sujaypatil96 closed 2 months ago

sujaypatil96 commented 3 months ago

Fixes #1940

sujaypatil96 commented 2 months ago

This PR is ready to be reviewed/merged @turbomam.

sujaypatil96 commented 2 months ago

Running the below command:

nmdc-schema git:(issue-1940) ✗ nmdc-ncbi-mapping package-specific-curation assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv
Optional NCBI Attribute names that do not have NMDC slot mappings: ['collection_method', 'isolation_source', 'neg_cont_type', 'omics_observ_id', 'pos_cont_type', 'ref_biomaterial', 'rel_to_oxygen', 'samp_collect_device', 'source_material_id']

Manual mappings for the above slots that can be filled out:

ncbi_biosample_attribute_name nmdc_schema_slot ignore justification for mapping
collection_method MAN_IGNORE
samp_collect_method samp_collec_method
isolation_source MAN_IGNORE
neg_cont_type MAN_IGNORE
pos_cont_type MAN_IGNORE
ref_biomaterial
rel_to_oxygen oxy_stat_samp
samp_collect_device samp_collec_device
source_material_id
sujaypatil96 commented 2 months ago

@turbomam requesting for a review on this PR. I suggest merging this in, and I will add my suggestions from the above comment to https://github.com/microbiomedata/nmdc-schema/blob/issue-1940/assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv once it has been created in main.

turbomam commented 2 months ago

do you still want this merge in here, as opposed to nmdc-runtime?

turbomam commented 2 months ago

I guess so since they are changes and not additions