v1.6

1.6

Table	Field	Change notes
called_variants_nanopore	variant_types	added STR as enumerated value
called_variants_pac_bio	variant_types	added STR as enumerated value
genetic_findings	experiment_id	added 'see_notes' and 'see_MOD' as example values (this field will be required for validation)
genetic_findings	variant_type	added more specific enumerated values (possibly with delimiter) to match 'called_variants' tables
genetic_findings	pos	added note describing that this is .vcf-style coordinates
genetic_findings	pos	updated conditional requirement to align with variant_type change
genetic_findings	GREGoR_variant_classification	required if known disease gene
genetic_findings	gene_disease_validity_notes	required if known disease gene
genetic_findings	gene_disease_validity_notes	added; not required
genetic_findings	VRS_ID	added; not required
experiment_rna_short_read	depletion_targets	added; not required
called_variants_nanopore	chrom	added; not required
called_variants_pac_bio	chrom	added; not required
called_variants_optical_mapping	chrom	added; not required
aligned_nanopore	num_reads	changed data type to float for large number support
aligned_nanopore	num_bases	changed data type to float for large number support
aligned_nanopore	num_aligned_reads	changed data type to float for large number support
aligned_nanopore	num_aligned_bases	changed data type to float for large number support
aligned_nanopore	read_length_mean	changed data type to float
aligned_pac_bio	num_reads	changed data type to float for large number support
aligned_pac_bio	num_bases	changed data type to float for large number support
aligned_pac_bio	num_aligned_reads	changed data type to float for large number support
aligned_pac_bio	num_aligned_bases	changed data type to float for large number support
aligned_pac_bio	read_length_mean	changed data type to float
analyte	analyte_type	added PBMC as enumerated value

v1.5

1.5

Table	Field	Change notes
genetic_findings	variant_type	added SV as allowable type
genetic_findings	sv_type	added; not required
genetic_findings	chrom	changed from required to conditional
genetic_findings	chrom_end	added; not required
genetic_findings	pos	changed from required to conditional
genetic_findings	pos_end	added; not required
genetic_findings	ref	changed from required to conditional
genetic_findings	alt	changed from required to conditional
genetic_findings	copy_number	added; not required
genetic_findings	gene_of_interest	renamed 'gene' field, made conditional, expanded notes
genetic_findings	hgvs	added; not required
genetic_findings	zygosity	added to list of allowable enumerations
genetic_findings	gene_disease_validity	added; not required
experiment_dna_short_read	sequencing_event_details	added; not required

GREGoR_Data_Model_v1.5.pdf

v1.4

1.4

Table	Field	Change notes
experiement_rna_short_read	total_reads	change data type to float to accommodate validation for numbers of reads >2^31
phenotype	syndromic	added; not required
aligned	aligned_file	will be populated by DCC in post-processing - no impact on data submitters.
aligned	aligned_file_index	will be populated by DCC in post-processing - no impact on data submitters.
experiment_dna_short_read	experiment_sample_id	field now required
experiment_dna_short_read	sequencing_event_details	added; not required
experiment_rna_short_read	total_reads	changed data type to float for large number support
experiment_nanopore	seq_library_prep_kit_method	added 'Unknown' ennumeration to allow for external data received where library prep kit is unknown
aligned_nanopore	quality_issues	added; not required
experiment_pac_bio	size_selection_method	added; not required
experiment_pac_bio	library_size	added; not required
experiment_pac_bio	smrt_cell_kit	added; not required
experiment_pac_bio	smrt_cell_id	added; not required
experiment_pac_bio	movie_name	added; not required
experiment_pac_bio	polymerase_kit	added; not required
experiment_pac_bio	sequencing_kit	added; not required
experiment_pac_bio	movie_length_hours	added; not required
experiment_pac_bio	includes_kinetics	added; not required
experiment_pac_bio	includes_CpG_methylation	added; not required
experiment_pac_bio	by_strand	added; not required

v1.3

Version 1.3 of the data model adds additional tables to support Pac Bio long read and ATAC short read technology. A new genetic_findings table tracks genetic findings and additional columns in the participant table track solve status. A new 'aligned' table summarizes all aligned read files for participants in the same table, similar to the experiment table.

Version	Table	Field	Change notes
1.3	genetic_findings	all	table added
1.3	experiment_pac_bio	all	table added
1.3	aligned_pac_bio	all	table added
1.3	aligned_pac_bio_set	all	table added
1.3	called_variants_pac_bio	all	table added
1.3	experiment_atac_short_read	all	table added
1.3	aligned_atac_short_read	all	table added
1.3	called_peaks_atac_short_read	all	table added
1.3	allele_specific_atac_short_read	all	table added
1.3	experiment	table_name	DCC added 'experiment_nanopore, experiment_pac_bio, and experiment_atac_short_read' as valid experiment types - no impact to data submitters.
1.3	aligned	all	table added - will be populated by DCC in post-processing - no impact on data submitters.
1.3	participant	solve_status	required field added
1.3	participant	missing_variant_case	required field added
1.3	participant	missing_variant_details	optional field added

v1.2

Version 1.2 of the data model adds additional tables to support nanopore technology.

Version	Table	Field	Change notes
1.2	experiment_nanopore	all	table added
1.2	aligned_nanopore	all	table added
1.2	aligned_nanopore_set	all	table added
1.2	called_variants_nanopore	all	table added
1.2	aligned_dna_short_read	all	DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters.
1.2	called_variants_dna_short_read	all	DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters.
1.2	aligned_rna_short_read	all	DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters.
1.2	aligned_nanopore	all	DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters.
1.2	called_variants_nanopore	all	DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters.