In what ways does the casing of GOLD vs gold matter? about nmdc-schema

[aclum]

@turbomam i think we can close this, all the gold prefixes are lowercase now.

[turbomam]

grep -R gold src/schema/*

src/schema/basic_slots.yaml: For example, when extracting study information for GOLD, the GOLD system has assigned a name/label.
src/schema/external_identifiers.yaml: GOLD: http://identifiers.org/gold/
src/schema/external_identifiers.yaml: gold_identifiers:
src/schema/external_identifiers.yaml: - https://gold.jgi.doe.gov/
src/schema/external_identifiers.yaml: gold_study_identifiers:
src/schema/external_identifiers.yaml: - gold_identifiers
src/schema/external_identifiers.yaml: pattern: "^GOLD:Gs[0-9]+$"
src/schema/external_identifiers.yaml: description: identifiers for corresponding project(s) in GOLD
src/schema/external_identifiers.yaml: - value: https://identifiers.org/gold:Gs0110115
src/schema/external_identifiers.yaml: - https://gold.jgi.doe.gov/studies
src/schema/external_identifiers.yaml: title: GOLD Study Identifiers
src/schema/external_identifiers.yaml: gold_biosample_identifiers:
src/schema/external_identifiers.yaml: - gold_identifiers
src/schema/external_identifiers.yaml: pattern: "^GOLD:Gb[0-9]+$"
src/schema/external_identifiers.yaml: description: identifiers for corresponding sample in GOLD
src/schema/external_identifiers.yaml: - value: https://identifiers.org/gold:Gb0312930
src/schema/external_identifiers.yaml: gold_sequencing_project_identifiers:
src/schema/external_identifiers.yaml: - gold_identifiers
src/schema/external_identifiers.yaml: pattern: "^GOLD:Gp[0-9]+$"
src/schema/external_identifiers.yaml: description: identifiers for corresponding sequencing project in GOLD
src/schema/external_identifiers.yaml: - value: https://identifiers.org/gold:Gp0108335
src/schema/external_identifiers.yaml: gold_analysis_project_identifiers:
src/schema/external_identifiers.yaml: - gold_identifiers
src/schema/external_identifiers.yaml: pattern: "^GOLD:Ga[0-9]+$"
src/schema/external_identifiers.yaml: description: identifiers for corresponding analysis project in GOLD
src/schema/external_identifiers.yaml: - value: https://identifiers.org/gold:Ga0526289
src/schema/external_identifiers.yaml: - in INSDC this is a run but it corresponds to a GOLD analysis
src/schema/nmdc.yaml: # GOLD: http://identifiers.org/gold/
src/schema/nmdc.yaml: - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833"
src/schema/nmdc.yaml: - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation
src/schema/nmdc.yaml: - removed id_prefixes value of GOLD, since we are now using pattern-based id validation
src/schema/nmdc.yaml: - could add GOLD and EBI's biosample definitions to the alt_descriptions?
src/schema/nmdc.yaml: - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation
src/schema/nmdc.yaml: - gold_biosample_identifiers
src/schema/nmdc.yaml: ## GOLD path fields
src/schema/nmdc.yaml: ## GOLD specific fields
src/schema/nmdc.yaml: gold_biosample_identifiers:
src/schema/nmdc.yaml: description: Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample
src/schema/nmdc.yaml: comments: This is the ID provided by GOLD that starts with 'GB'
src/schema/nmdc.yaml: display_hint: Provide the GOLD biosample IDs associated with this biosample.
src/schema/nmdc.yaml: - gold_study_identifiers
src/schema/nmdc.yaml: - "sample GOLD link https://identifiers.org/gold:Gs0110115"
src/schema/nmdc.yaml: - "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id"
src/schema/nmdc.yaml: - The ID prefix for objects coming from GOLD will be gold:Gp
src/schema/nmdc.yaml: - gold_sequencing_project_identifiers
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_structural_annotation.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_structural_annotation_stats.json'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_functional_annotation.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_imgap.info'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_proteins.faa'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_ec.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_ko.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_pairedMapped.sam.gz'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_assembly.contigs.fasta'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_pairedMapped_sorted.bam.cov'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_contig_names_mapping.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_tigrfam.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_crt.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_genemark.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_prodigal.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_trna.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_rfam.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_rfam_ncrna_tmrna.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_ko_ec.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_product_names.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_gene_phylogeny.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_gene_phylogeny.tsv'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_cog.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_cath_funfam.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_supfam.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_smart.gff'
src/schema/nmdc.yaml: file_name_pattern: '[GOLD-AP]_pfam.gff'
src/schema/nmdc.yaml: ## GOLD PATHS
src/schema/nmdc.yaml: gold_path_field:
src/schema/nmdc.yaml: This is a grouping for any of the gold path fields
src/schema/nmdc.yaml: is_a: gold_path_field
src/schema/nmdc.yaml: Ecosystem is in position 1/5 in a GOLD path.
src/schema/nmdc.yaml: of organisms in a given environment. The GOLD Ecosystem at the top of the five-level
src/schema/nmdc.yaml: see_also: https://gold.jgi.doe.gov/help
src/schema/nmdc.yaml: is_a: gold_path_field
src/schema/nmdc.yaml: is isolated. Ecosystem category is in position 2/5 in a GOLD path.
src/schema/nmdc.yaml: see_also: https://gold.jgi.doe.gov/help
src/schema/nmdc.yaml: is_a: gold_path_field
src/schema/nmdc.yaml: type is in position 3/5 in a GOLD path.
src/schema/nmdc.yaml: see_also: https://gold.jgi.doe.gov/help
src/schema/nmdc.yaml: is_a: gold_path_field
src/schema/nmdc.yaml: into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
src/schema/nmdc.yaml: see_also: https://gold.jgi.doe.gov/help
src/schema/nmdc.yaml: is_a: gold_path_field
src/schema/nmdc.yaml: Specific ecosystem is in position 5/5 in a GOLD path.
src/schema/nmdc.yaml: see_also: https://gold.jgi.doe.gov/help
src/schema/nmdc.yaml: description: A unique id representing the GOLD classifers associated with a sample.
src/schema/nmdc.yaml: - "maps to gold:salinity"
src/schema/sample_prep.yaml:# GOLD: http://identifiers.org/gold/
src/schema/workflow_execution_activity.yaml: - gold_analysis_project_identifiers
src/schema/workflow_execution_activity.yaml: - gold_analysis_project_identifiers

[turbomam]

grep -i -R gold src/data/*

src/data/invalid/Database-Biosample-invalid_range.yaml: gold_biosample_identifiers:
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gb0101224
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gs0128849
src/data/invalid/Database-Biosample-invalid_range.yaml: gold_biosample_identifiers:
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gb0101225
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gs0128849
src/data/invalid/Database-Biosample-invalid_range.yaml: gold_biosample_identifiers:
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gb0101226
src/data/invalid/Database-Biosample-invalid_range.yaml: - gold:Gs0128849
src/data/invalid/Biosample-invalid_fire.yaml: - gold:Gs0110115
src/data/invalid/Database-biosamples-lat_lon-with-GLV-missing-longitude.yaml: - gold:Gs0110115
src/data/invalid/Database-invalid-studies.yaml: id: gold:Gs0110115
src/data/invalid/Database-invalid-studies.yaml: - id: gold:Gs0110132
src/data/invalid/Database-invalid-studies.yaml: - id: gold:Gs0112340
src/data/invalid/Database-biosamples-rna-in-plate-invalid-well-val.yaml: - gold:Gs0110115
src/data/invalid/Database-biosamples-dna-in-tube-with-well-value.yaml: - gold:Gs0110115
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold_biosample_identifiers:
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_mismatch_regex.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold:Gb0101225
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold_biosample_identifiers:
src/data/invalid/Database-biosample_mismatch_regex.yaml: - gold:Gs0128849
src/data/invalid/Biosample-missing-id.yaml: - gold:Gs0110115
src/data/invalid/Database-biosamples-rna-in-plate-no-well-val.yaml: - gold:Gs0110115
src/data/invalid/OmicsProcessing-invalid-omics-type.yaml: - gold:Gp0108335
src/data/invalid/OmicsProcessing-invalid-omics-type.yaml: - gold:Gb0108335
src/data/invalid/OmicsProcessing-invalid-omics-type.yaml: - gold:Gs0112340
src/data/invalid/Database-biosamples-lat_lon-with-GLV-missing-latitude.yaml: - gold:Gs0110115
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gb0101224
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gb0101225
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gb0101225
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gb0101226
src/data/invalid/Database-biosample_single_multi_value_mixup.yaml: - gold:Gs0128849
src/data/invalid/Database-biosamples-dna-in-bucket.yaml: - gold:Gs0110115
src/data/invalid/Database-biosample_undeclared_slot.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gb0101224
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_undeclared_slot.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gb0101225
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gs0128849
src/data/invalid/Database-biosample_undeclared_slot.yaml: gold_biosample_identifiers:
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gb0101226
src/data/invalid/Database-biosample_undeclared_slot.yaml: - gold:Gs0128849
src/data/invalid/Database-biosamples-rna-in-tube-with-well-value.yaml: - gold:Gs0110115
src/data/invalid/Biosample-incomplete_napa_id.yaml:gold_biosample_identifiers:
src/data/invalid/Biosample-incomplete_napa_id.yaml: - gold:Gb0101224
src/data/invalid/Biosample-incomplete_napa_id.yaml: - gold:Gs0110115
src/data/invalid/Database-biosamples-dna-in-plate-invalid-well-val.yaml: - gold:Gs0110115
src/data/invalid/MetagenomeSequencingActivity-no_parthood.yaml:was_informed_by: gold:Gp0213371
src/data/invalid/Database-biosamples-rna-in-bucket.yaml: - gold:Gs0110115
src/data/invalid/MetagenomeSequencingActivity-bad_id.yaml:was_informed_by: gold:Gp0213371
src/data/invalid/Biosample-non_boolean_embargo.yaml: - gold:Gs0110115
src/data/invalid/Database-biosamples-dna-in-plate-no-well-val.yaml: - gold:Gs0110115
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gp0108335
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gb0108335
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gs0112340
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gp0108340
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gb0108340
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gs0112340
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gp0108341
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gb0108341
src/data/invalid/Database-invalid-omics-processing.yaml: - gold:Gs0112340
src/data/invalid/OmicsProcessing-no-id.yaml: - gold:Gp0108335
src/data/invalid/OmicsProcessing-no-id.yaml: - gold:Gb0108335
src/data/invalid/OmicsProcessing-no-id.yaml: - gold:Gs0112340
src/data/invalid/Biosample-invalid-embargoed.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-1.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-1.yaml: - GOLD:Gb0101224
src/data/valid/Database-biosamples-1.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-1.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-1.yaml: - GOLD:Gb0101224
src/data/valid/Database-biosamples-1.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-1.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-1.yaml: - GOLD:Gb0101225
src/data/valid/Database-biosamples-1.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-1.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-1.yaml: - GOLD:Gb0101226
src/data/valid/Database-biosamples-1.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0305833
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0291692
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0291582
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0305834
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0291693
src/data/valid/Database-biosamples-sites.yaml: gold_biosample_identifiers:
src/data/valid/Database-biosamples-sites.yaml: - GOLD:Gb0291583
src/data/valid/Database-mags-activities.yaml: was_informed_by: gold:Gp0115663
src/data/valid/Database-mags-activities.yaml: was_informed_by: gold:Gp0115664
src/data/valid/Study-exhaustive.yaml:gold_study_identifiers:
src/data/valid/Study-exhaustive.yaml: - GOLD:Gs12345
src/data/valid/Study-exhaustive.yaml: - GOLD:Gs90909
src/data/valid/Database-biosamples-rna-in-tube.yaml: - gold:Gs0110115
src/data/valid/Database-multiple-paths.yaml: - gold:Gs0110115
src/data/valid/Database-multiple-paths.yaml: - gold:Gs0110115
src/data/valid/Database-multiple-paths.yaml: - gold:Gp0108335
src/data/valid/Database-multiple-paths.yaml: - gold:Gb0108335
src/data/valid/Database-multiple-paths.yaml: - gold:Gs0112340
src/data/valid/Database-metagenome-assembly.yaml: was_informed_by: gold:Gp0061273
src/data/valid/Database-metagenome-assembly.yaml: was_informed_by: gold:Gp0061274
src/data/valid/Database-metagenome-assembly.yaml: was_informed_by: gold:Gp0061275
src/data/valid/Database-omics-processings.yaml: - gold:Gp0108335
src/data/valid/Database-omics-processings.yaml: - gold:Gb0108335
src/data/valid/Database-omics-processings.yaml: - gold:Gs0112340
src/data/valid/Database-omics-processings.yaml: - gold:Gp0108340
src/data/valid/Database-omics-processings.yaml: - gold:Gb0108340
src/data/valid/Database-omics-processings.yaml: - gold:Gs0112340
src/data/valid/Database-omics-processings.yaml: - gold:Gp0108341
src/data/valid/Database-omics-processings.yaml: - gold:Gb0108341
src/data/valid/Database-omics-processings.yaml: - gold:Gs0112340
src/data/valid/Database-biosamples-rna-in-plate-valid-well-val.yaml: - gold:Gs0110115
src/data/valid/DataObject-1.yaml:description: Metagenome Contig Coverage Stats for gold:Gp0061273
src/data/valid/Biosample-soil_horizon.yaml: - gold:Gs0110115
src/data/valid/ReadQcAnalysisActivity-1.yaml:was_informed_by: "gold:Gp0061273"
src/data/valid/Database-biosamples-minimal.yaml: - gold:Gs0110115
src/data/valid/Biosample-exhasutive.yaml:gold_biosample_identifiers:
src/data/valid/Biosample-exhasutive.yaml: - GOLD:Gb123456789
src/data/valid/Biosample-exhasutive.yaml: - GOLD:Gb90909090
src/data/valid/DataObject-2.yaml:description: Assembled scaffold fasta for gold:Gp0061273
src/data/valid/Biosample-embargoed.yaml: - gold:Gs0110115
src/data/valid/Database-with-MetagenomeSequencingActivity.yaml: was_informed_by: gold:Gp0213371
src/data/valid/Biosample-minimal-2.yaml: - gold:Gs0110115
src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml:gold_biosample_identifiers:
src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml: - GOLD:Gb123456789
src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml: - GOLD:Gb90909090
src/data/valid/OmicsProcessing-1.yaml: - gold:Gp0108335
src/data/valid/OmicsProcessing-1.yaml: - gold:Gb0108335
src/data/valid/OmicsProcessing-1.yaml: - gold:Gs0112340
src/data/valid/Database-study-set-with-gnps-id.yaml: gold_study_identifiers:
src/data/valid/Database-study-set-with-gnps-id.yaml: - GOLD:Gs0128849
src/data/valid/DataObject-3.yaml:description: Metagenome Contig Coverage Stats for gold:Gp0061273
src/data/valid/Database-nmdc-example.yaml: gold_study_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0128849
src/data/valid/Database-nmdc-example.yaml: gold_study_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0130354
src/data/valid/Database-nmdc-example.yaml: gold_study_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0134277
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gp0225767
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0157174
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0130354
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gp0208560
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0150408
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0128849
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gp0306221
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0188037
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0134277
src/data/valid/Database-nmdc-example.yaml: gold_biosample_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0150408
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0128849
src/data/valid/Database-nmdc-example.yaml: gold_biosample_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0157174
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0128849
src/data/valid/Database-nmdc-example.yaml: gold_biosample_identifiers:
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gb0188037
src/data/valid/Database-nmdc-example.yaml: - GOLD:Gs0128849
src/data/valid/Biosample-with-fire.yaml: - gold:Gs0110115
src/data/valid/Biosample-minimal.yaml: - gold:Gs0110115
src/data/valid/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.yaml:was_informed_by: gold:Gp0213371
src/data/valid/Database-biosamples-dna-in-tube.yaml: - gold:Gs0110115
src/data/valid/Database-biosamples-dna-in-plate-valid-well-val.yaml: - gold:Gs0110115