diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a51cf4..91b2050 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,32 +2,33 @@ ## 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 |changed allowable values to match other 'called_variants' tables (SNV, INDEL as separate values posssibly with delimiter instead of SNV/INDEL | -|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 | +|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 | ## 1.5.2 diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 33ea412..231206a 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -343,10 +343,10 @@ "column": "variant_type", "required": true, "data_type": "enumeration", - "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], + "enumerations": ["SNV/INDEL", "SV", "RE", "SNV", "INDEL", "CNV", "MEI", "STR"], "multi_value_delimiter": "|", "examples": "SNV|CNV", - "notes": "SNV: single nucelotide variants\nINDEL: short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions" + "notes": "SNV/INDEL: single nucelotide variants or short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions" }, { "column": "sv_type", @@ -638,7 +638,7 @@ "required": true, "description": "analyte derived from the primary_biosample. The actual thing you're sticking into a machine to analyze/sequence", "data_type": "enumeration", - "enumerations": ["DNA", "RNA", "cDNA", "blood plasma", "frozen whole blood", "high molecular weight DNA", "urine"], + "enumerations": ["DNA", "RNA", "cDNA", "blood plasma", "frozen whole blood", "high molecular weight DNA", "urine", "PBMC"], "examples": "DNA" }, {