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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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In what ways does the casing of GOLD vs gold matter? #913

Closed turbomam closed 11 months ago

turbomam commented 1 year ago

@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 commented 1 year ago 
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 commented 1 year ago 
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 commented 11 months ago

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