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change log for v1.4
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@smgogarten
smgogarten committed Jan 31, 2024
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65 changes: 49 additions & 16 deletions CHANGELOG.md
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# Change log

## 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 |


## 1.3

|Table |Field |Change notes |
|:-------------------------------|:-----------------------|:---------------------------------------------------------------------------------------------------------------------------------------------|
|genetic_findings |all |table added |
|experiment_pac_bio |all |table added |
|aligned_pac_bio |all |table added |
|aligned_pac_bio_set |all |table added |
|called_variants_pac_bio |all |table added |
|experiment_atac_short_read |all |table added |
|aligned_atac_short_read |all |table added |
|called_peaks_atac_short_read |all |table added |
|allele_specific_atac_short_read |all |table added |
|experiment |table_name |DCC added 'experiment_nanopore, experiment_pac_bio, and experiment_atac_short_read' as valid experiment types - no impact to data submitters. |
|aligned |all |table added - will be populated by DCC in post-processing - no impact on data submitters. |
|participant |solve_status |required field added |
|participant |missing_variant_case |required field added |
|participant |missing_variant_details |optional field added |
|Table |Field |Change notes |
|:-------------------------------|:------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------|
|genetic_findings |all |table added |
|experiment_pac_bio |all |table added |
|aligned_pac_bio |all |table added |
|aligned_pac_bio_set |all |table added |
|called_variants_pac_bio |all |table added |
|experiment_atac_short_read |all |table added |
|aligned_atac_short_read |all |table added |
|called_peaks_atac_short_read |all |table added |
|allele_specific_atac_short_read |all |table added |
|experiment |table_name |DCC added 'experiment_nanopore, experiment_pac_bio, and experiment_atac_short_read' as valid experiment types - no impact to data submitters. |
|aligned |all |table added - will be populated by DCC in post-processing - no impact on data submitters. |
|participant |solve_status |required field added |
|participant |missing_variant_case |required field added |
|participant |missing_variant_details |optional field added |
|genetic_findings |hgvsc |added; not required |
|genetic_findings |hgvsp |added; not required |
|genetic_findings |zygosity |added; not required |
|genetic_findings |known_condition_name |required if gene_known_for_phenotype = Known |
|genetic_findings |condition_id |required if gene_known_for_phenotype = Known |
|genetic_findings |condition_inheritance |required if gene_known_for_phenotype = Known |
|genetic_findings |partial_contribution_explained |required if phenotype_contribution = Partial |


## 1.2
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -3,6 +3,6 @@ A repository for version control of the [GREGoR Consortium](https://gregorconsor

The JSON is defined to be easily translated to Database Markup Language (DBML) using the [AnvilDataModels](https://github.com/UW-GAC/AnvilDataModels) R package. The DBML file is rendered using [dbdiagram.io](https://dbdiagram.io/d/624227bbbed6183873142297) for visualization.

Additional documentation and information is available via the google sheets-based [data dictionary](https://docs.google.com/spreadsheets/d/1mZlJ9IauaVNiJ6f2Q14pg6rGEpWVrAjMJmAZ_FioVTY) for the data model. In case of any discrepency, the .json file in this repository is the authoritative version of the Consortium data model.
Additional documentation and information is available via the google sheets-based [data dictionary](https://docs.google.com/spreadsheets/d/1NcB5pz7rWr2AJpjmDFu6v5E5pGVWmAoaS2kH-pF86H8) for the data model. In case of any discrepency, the .json file in this repository is the authoritative version of the Consortium data model.

![GREGoR identifiers diagram](GREGoR_identifiers_diagram.png)
2 changes: 1 addition & 1 deletion change_log.R
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Expand Up @@ -2,7 +2,7 @@ library(googlesheets4)
library(dplyr)
library(readr)

url <- "https://docs.google.com/spreadsheets/d/1mZlJ9IauaVNiJ6f2Q14pg6rGEpWVrAjMJmAZ_FioVTY"
url <- "https://docs.google.com/spreadsheets/d/1NcB5pz7rWr2AJpjmDFu6v5E5pGVWmAoaS2kH-pF86H8"

log <- read_sheet(url, sheet="Change Log") %>%
filter(!is.na(Version)) %>%
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