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Merge pull request #64 from HDRUK/GAT-5259
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Update demographics ages, omics formatting and required fields
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@BSnelling
BSnelling authored Oct 7, 2024
2 parents ac923b7 + 6b4a86c commit acd8f43
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36 changes: 18 additions & 18 deletions docs/GWDM/2.0.form.json
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Expand Up @@ -1419,7 +1419,7 @@
"5-9 years",
"10-14 years",
"15-19 years",
"20-14 years",
"20-24 years",
"25-29 years",
"30-34 years",
"35-39 years",
Expand All @@ -1434,7 +1434,7 @@
"80-84 years",
"85-89 years",
"90-94 years",
"65-99 years",
"95-99 years",
"100+ years"
]
},
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"type": "string",
"options": [
"NMR spectroscopy",
"mass-spectrometry",
"whole genome sequencing",
"exome sequencing",
"genotyping by array",
"transcriptome profiling by high-throughput sequencing",
"transcriptome profiling by array",
"amplicon sequencing",
"methylation binding domain sequencing",
"methylation profiling by high-throughput sequencing",
"genomic variant calling",
"chromatin accessibility profiling by high-throughput sequencing",
"histone modification profiling by high-throughput sequencing",
"chromatin immunoprecipitation sequencing",
"whole genome shotgun sequencing",
"whole transcriptome sequencing",
"targeted mutation analysis"
"Mass-spectrometry",
"Whole genome sequencing",
"Exome sequencing",
"Genotyping by array",
"Transcriptome profiling by high-throughput sequencing",
"Transcriptome profiling by array",
"Amplicon sequencing",
"Methylation binding domain sequencing",
"Methylation profiling by high-throughput sequencing",
"Genomic variant calling",
"Chromatin accessibility profiling by high-throughput sequencing",
"Histone modification profiling by high-throughput sequencing",
"Chromatin immunoprecipitation sequencing",
"Whole genome shotgun sequencing",
"Whole transcriptome sequencing",
"Targeted mutation analysis"
]
},
"location": "omics.assay"
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4 changes: 2 additions & 2 deletions docs/GWDM/2.0.md
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Expand Up @@ -1391,7 +1391,7 @@ None

| title | guidance | is_list | required | type |
|:--------|:-----------|:----------|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Age bin | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']"] |
| Age bin | | False | True | ["AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']"] |



Expand Down Expand Up @@ -1495,7 +1495,7 @@ The specific 'omics assay that generated the dataset.

| title | guidance | is_list | required | type |
|:------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------|:-----------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']", 'null'] |
| Omics assay | The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry. | False | False | ["Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']", 'null'] |



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4 changes: 2 additions & 2 deletions docs/GWDM/2.0.structure.json
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Expand Up @@ -1898,7 +1898,7 @@
"guidance": "",
"examples": null,
"type": [
"AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-14 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','65-99 years','100+ years']"
"AgeEnum['0-6 days','7-27 days','1-11 months','1-4 years','5-9 years','10-14 years','15-19 years','20-24 years','25-29 years','30-34 years','35-39 years','40-44 years','45-49 years','50-54 years','55-59 years','60-64 years','65-69 years','70-74 years','75-79 years','80-84 years','85-89 years','90-94 years','95-99 years','100+ years']"
],
"is_list": false,
"is_optional": false
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"guidance": "The specific 'omics assay that generated the dataset. If the assay used to generate your dataset is not listed, please contract the gateway team by submitting an enquiry.",
"examples": null,
"type": [
"Assay['NMR spectroscopy','mass-spectrometry','whole genome sequencing','exome sequencing','genotyping by array','transcriptome profiling by high-throughput sequencing','transcriptome profiling by array','amplicon sequencing','methylation binding domain sequencing','methylation profiling by high-throughput sequencing','genomic variant calling','chromatin accessibility profiling by high-throughput sequencing','histone modification profiling by high-throughput sequencing','chromatin immunoprecipitation sequencing','whole genome shotgun sequencing','whole transcriptome sequencing','targeted mutation analysis']",
"Assay['NMR spectroscopy','Mass-spectrometry','Whole genome sequencing','Exome sequencing','Genotyping by array','Transcriptome profiling by high-throughput sequencing','Transcriptome profiling by array','Amplicon sequencing','Methylation binding domain sequencing','Methylation profiling by high-throughput sequencing','Genomic variant calling','Chromatin accessibility profiling by high-throughput sequencing','Histone modification profiling by high-throughput sequencing','Chromatin immunoprecipitation sequencing','Whole genome shotgun sequencing','Whole transcriptome sequencing','Targeted mutation analysis']",
"null"
],
"is_list": false,
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40 changes: 20 additions & 20 deletions docs/HDRUK/3.0.0.form.json
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Expand Up @@ -357,7 +357,7 @@
"location": "documentation.inPipeline"
},
{
"required": false,
"required": true,
"title": "Geographic coverage",
"description": "The geographical area covered by the dataset. It is recommended that links are to entries in one of the recommended standards:\\n- For locations in the UK: [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about)\\n- For locations in other countries: [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes)",
"guidance": "- The geographical area covered by the dataset.\\n- Please provide a valid location.\\n- For locations in the UK, this location should conform to [ONS standards](https://geoportal.statistics.gov.uk/datasets/ons::index-of-place-names-in-great-britain-november-2021/about).\\n- For locations in other countries we use [ISO 3166-1 & ISO 3166-2](https://github.com/HDRUK/reference-codes).",
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"location": "provenance.temporal.distributionReleaseDate"
},
{
"required": false,
"required": true,
"title": "Start date",
"description": "The start of the time period that the dataset provides coverage for. If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.",
"guidance": "- The start of the time period that the dataset provides coverage for.\\n- If there are multiple cohorts in the dataset with varying start dates, please provide the earliest date and use the description or the media attribute to provide more information.",
Expand Down Expand Up @@ -1668,7 +1668,7 @@
"5-9 years",
"10-14 years",
"15-19 years",
"20-14 years",
"20-24 years",
"25-29 years",
"30-34 years",
"35-39 years",
Expand All @@ -1683,7 +1683,7 @@
"80-84 years",
"85-89 years",
"90-94 years",
"65-99 years",
"95-99 years",
"100+ years"
]
},
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"type": "string",
"options": [
"NMR spectroscopy",
"mass-spectrometry",
"whole genome sequencing",
"exome sequencing",
"genotyping by array",
"transcriptome profiling by high-throughput sequencing",
"transcriptome profiling by array",
"amplicon sequencing",
"methylation binding domain sequencing",
"methylation profiling by high-throughput sequencing",
"genomic variant calling",
"chromatin accessibility profiling by high-throughput sequencing",
"histone modification profiling by high-throughput sequencing",
"chromatin immunoprecipitation sequencing",
"whole genome shotgun sequencing",
"whole transcriptome sequencing",
"targeted mutation analysis"
"Mass-spectrometry",
"Whole genome sequencing",
"Exome sequencing",
"Genotyping by array",
"Transcriptome profiling by high-throughput sequencing",
"Transcriptome profiling by array",
"Amplicon sequencing",
"Methylation binding domain sequencing",
"Methylation profiling by high-throughput sequencing",
"Genomic variant calling",
"Chromatin accessibility profiling by high-throughput sequencing",
"Histone modification profiling by high-throughput sequencing",
"Chromatin immunoprecipitation sequencing",
"Whole genome shotgun sequencing",
"Whole transcriptome sequencing",
"Targeted mutation analysis"
]
},
"location": "omics.assay"
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