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In what ways does the casing of GOLD vs gold matter? #913

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turbomam opened this issue May 26, 2023 · 3 comments
Closed

In what ways does the casing of GOLD vs gold matter? #913

turbomam opened this issue May 26, 2023 · 3 comments

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@turbomam
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turbomam commented May 26, 2023 •
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@aclum pointed out that there are case mismatches between the way GOLD is represented in the schema (slot patterns, for example), data, primary resources (like at lest one GOLD API may require inputs to be in a particular case), and third party resolvers

Bioregistry has a https://bioregistry.io/registry/gold page

identifiers.org has a https://registry.identifiers.org/registry/gold page

https://bioregistry.io/gold:Gs0110115 and https://identifiers.org/gold:Gs0000008 resolve to https://gold.jgi.doe.gov/study?id=Gs0110115

The public GOLD API home is here: https://gold-ws.jgi.doe.gov/

I can log in with my JGI credentials and use the swagger interface at https://gold-ws.jgi.doe.gov/swagger-ui/index.html

The following link, with a local id and not GOLD prefix works: https://gold-ws.jgi.doe.gov/api/v1/studies?studyGoldId=Gs0110115

There is also some separate API that specifically allows NMDC users to retrieve GOLD information

@sujaypatil96 can you please provide information bout which GOLD API you use? Does it require queries to include the GOLD prefix? In what case should GOLD/gold be written?
@turbomam turbomam mentioned this issue May 26, 2023
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@turbomam
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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
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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

@aclum aclum mentioned this issue Jun 9, 2023
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aclum commented Oct 26, 2023

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

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