This directory holds SSSOM files used to define mappings.

Might require moving to a better location.

• biosample_env_package_normalizastion.tsv
  • Counts all of the env_package values submitted to NCBI Biosample Metadata and provides mappings to EnvPackage from https://www.ncbi.nlm.nih.gov/biosample/docs/packages/?format=xml where possible. Lot of overlap with env_package.pattern from mixs.yaml, but not identical. EnvPackageDisplay may actually provide better overlap.
  • 14,083,847 out of 14,300,584 biosamples have no env_package annotation.
  • Roughly 50k biosamples each are annotated with host-associated and human-gut. Are those of interest to NMDC?
  • 16,367 samples are annotated with water
  • TODO: what's the correlation of water annotated biosamples with biosamples whose taxonomy_id indicates an unidentified/environmental/metagenome sample?
• per_biosample_scoped_ebs_mapping_results.tsv
  • This file accounts for the fact that biosamples can be annotated with a pipe-delimited list of terms in MIxS triad columns like env_broad_scale. See https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN13905271
  • Otherwise, it is just a merger of biosample_ebs_water_packages_unclassified_taxa_sssom.tsv with the NCBI Biosample metadata
  • Based on recent discussions with Chris M, the mapped IDs and labels have not been re-assembled into the label [ID] format yet
  • Therefore BIOSAMPLE:SAMN13905271, which officially has an env_broad_scale annotation of 'Marine Biome [ENVO:00000447]|Archipelago [ENVO:00000220]' is assigned the IDs ENVO:00000447|ENVO:00000220 and the labels marine biome|archipelago