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 toEnvPackage
from https://www.ncbi.nlm.nih.gov/biosample/docs/packages/?format=xml where possible. Lot of overlap withenv_package.pattern
frommixs.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
andhuman-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 whosetaxonomy_id
indicates an unidentified/environmental/metagenome sample?
- Counts all of the
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 anenv_broad_scale
annotation of 'Marine Biome [ENVO:00000447]|Archipelago [ENVO:00000220]' is assigned the IDsENVO:00000447|ENVO:00000220
and the labelsmarine biome|archipelago
- This file accounts for the fact that biosamples can be annotated with a pipe-delimited list of terms in MIxS triad columns like