Update and validate gold:Gs0114663 / nmdc:sty-11-aygzgv51 Riverbed sediment (metabolomics, metagenomes, NOM, proteomics)

[mbthornton-lbl]

Omics Type(s): metagenomes, metatranscriptomes, NOM

Steps:

MetaG / MetaT:
Re-ID process (nmdc_automation) re_id_tool.py commands:

• update-study requires using identifiers mapping file from repo
• extract-records
• process-records (mint new IDs)
• process-records --update-links (make updates on filesystem)
• ingest-records
• delete-old-records

Metabolomics:
handled by update-study

NOM:
handled by update-study

proteomics:

• add missing data_object_set records via json:submit(proteomics raw data)
  nmdc.data_objects_set.stegen.metap.2024-04-30-03.json
• changesheets:submit to update omics_processing_set has_output records, using this tsv file
• metap_records_delete.py if not already run for nmdc:sty-11-33fbta56 - can be run before or after two steps above.

Validation process (nmdc_schema):

• Extract Study data as YAML with nmdc_database_tools.py extract-study
• Validate to current schema with linkml-validate

Data portal validation:

• 85 samples, 34 metabolomics, 50 metagenome, 294 NOM, 33 proteomics

expected number of biosample_set records: 85
expected number of omics_processing_set records: 411

[mbthornton-lbl]

% linkml-validate -s local/nmdc-schemav10.1.4.yaml local/nmdc:sty-11-aygzgv51.yaml
No issues found