SARS-CoV-2 viral sequencing data (COG-UK data) - Lineage/Variant Data - Scotland

Summary

Abstract

Summary of SARS-CoV-2 lineages and mutations

Contact point

phs.edris@phs.scot
Digital object identifier (DOI)

Not available

Keywords

Genome Covid-19

Publisher

Name

Public Health Scotland
Logo

Not available
Description

Not available
Contact point

Not available

Documentation

Description

File contains basic public metadata, including sequence_name, location, date, pangolin lineage assignment, version and associated scores, scorpio VOC/VUI constellation call and associated scores, key spike protein mutations calls and a list of all nucleotide mutations found.

Associated media
- Available resource files can be downloaded below.
  
  https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/overview/what-is-edris/
Is part of
- Not available
Landing page

https://healthdatagateway.org/dataset/72

Coverage

Spatial

Spatial coverage

United Kingdom, Scotland
Geographic levels

Not available

Temporal

Start date

28/02/2021
End date

Not available
Frequency

Weekly
Distribution release date

19/08/2021

Provenance

Purpose

Other
Source

Lims
Collection situation

Other

Access and governance

Conditions of access

Genetic studies only

Requesting access to this data

This is a secure dataset that can only be accessed by researchers from approved organisations.

Find out how to apply to access this dataset

Usage

Conditions of use

Project-specific restrictions
Resource creator

COG-UK
Is referenced by
Not available

Access

Access rights

https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/services-we-offer/
Access service

Scottish National Safe Haven / Trusted Research Environment https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/national-safe-haven-nsh/
Jurisdiction

GB-SCT
Data controller

Public Health Scotland
Data processor

Public Health Scotland

Format and standards

Language

English
Format

Csv

Enrichment and linkage

Related datasets
- Not available
Linkage opportunity

Not available
Tools
- Not available

Synthetic data

Synthetic data is not yet available for this dataset.

Technical information

A JSON file is available with further technical information. This can include details of variables and data classes contained in the dataset.

View technical information

Preview of JSON file

{
  "linkage": {
    "associatedMedia": "https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/overview/what-is-edris/"
  },
  "summary": {
    "title": "SARS-CoV-2 viral sequencing data (COG-UK data) - Lineage/Variant Data - Scotland",
    "abstract": "Summary of SARS-CoV-2 lineages and mutations",
    "keywords": "Genome;,;Covid-19",
    "publisher": {
      "name": "Public Health Scotland",
      "gatewayId": "c40be7ce-f0ca-4fd8-b63c-0632593d2507"
    },
    "inPipeline": "Not available",
    "shortTitle": "SARS-CoV-2 viral sequencing data (COG-UK data) - Lineage/Variant Data - Scotland",
    "datasetType": "Health and disease",
    "description": "File contains basic public metadata, including sequence_name, location, date, pangolin lineage assignment, version and associated scores, scorpio VOC/VUI constellation call and associated scores, key spike protein mutations calls and a list of all nucleotide mutations found.",
    "contactPoint": "phs.edris@phs.scot",
    "datasetSubType": "Not applicable",
    "populationSize": -1
  },
  "coverage": {
    "pathway": "No",
    "spatial": "United Kingdom,Scotland",
    "followUp": "Other",
    "typicalAgeRange": "0-150"
  },
  "required": {
    "issued": "2024-10-08T11:28:19.10964Z",
    "version": "6.0.0",
    "modified": "2024-10-08T11:28:19.109652Z",
    "gatewayId": "72",
    "revisions": [
      {
        "url": "https://web.prod.hdruk.cloud//dataset/72?version=1.0.0",
        "version": "1.0.0"
      }
    ],
    "gatewayPid": "98a93af0-cac8-4826-977b-6c5fd9e1376f"
  },
  "provenance": {
    "origin": {
      "source": "LIMS",
      "purpose": "Other",
      "imageContrast": "Not stated",
      "collectionSituation": "Other"
    },
    "temporal": {
      "timeLag": "1-2 weeks",
      "startDate": "2021-02-28",
      "accrualPeriodicity": "Weekly",
      "distributionReleaseDate": "2021-08-19"
    }
  },
  "observations": [
    {
      "observedNode": "Events",
      "measuredValue": 721005,
      "observationDate": "2021-08-20",
      "measuredProperty": "Count"
    }
  ],
  "accessibility": {
    "usage": {
      "resourceCreator": {
        "name": "COG-UK"
      },
      "dataUseLimitation": "Genetic studies only",
      "dataUseRequirement": "Project-specific restrictions"
    },
    "access": {
      "accessRights": "https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/services-we-offer/",
      "jurisdiction": "GB-SCT",
      "accessService": "Scottish National Safe Haven / Trusted Research Environment\n\nhttps://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/national-safe-haven-nsh/",
      "dataProcessor": "Public Health Scotland",
      "dataController": "Public Health Scotland",
      "deliveryLeadTime": "2-4 weeks",
      "accessRequestCost": "https://publichealthscotland.scot/services/data-research-and-innovation-services/electronic-data-research-and-innovation-service-edris/cost-of-services/",
      "accessServiceCategory": "TRE/SDE"
    },
    "formatAndStandards": {
      "formats": "csv",
      "languages": "en",
      "vocabularyEncodingSchemes": "OTHER"
    }
  },
  "structuralMetadata": [
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "PSEUDO-ANONYMISED ID NUMBER",
          "dataType": "character",
          "sensitive": false,
          "description": "PSEUDO-ANONYMISED ID NUMBER"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "sequence_name",
          "dataType": "character",
          "sensitive": false,
          "description": "sequence_name"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "shortid",
          "dataType": "character",
          "sensitive": false,
          "description": "shortid"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "country",
          "dataType": "character",
          "sensitive": false,
          "description": "country"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "adm1",
          "dataType": "character",
          "sensitive": false,
          "description": "adm1"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "is_pillar_2",
          "dataType": "character",
          "sensitive": false,
          "description": "is_pillar_2"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "sample_date",
          "dataType": "Date",
          "sensitive": false,
          "description": "sample_date"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "epi_week",
          "dataType": "character",
          "sensitive": false,
          "description": "epi_week"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "lineage",
          "dataType": "character",
          "sensitive": false,
          "description": "lineage"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "lineage_support",
          "dataType": "character",
          "sensitive": false,
          "description": "lineage_support"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "lineages_version",
          "dataType": "character",
          "sensitive": false,
          "description": "lineages_version"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "variants",
          "dataType": "character",
          "sensitive": false,
          "description": "variants"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "d614g",
          "dataType": "character",
          "sensitive": false,
          "description": "d614g"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "n439k",
          "dataType": "character",
          "sensitive": false,
          "description": "n439k"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "p323l",
          "dataType": "character",
          "sensitive": false,
          "description": "p323l"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "a222v",
          "dataType": "character",
          "sensitive": false,
          "description": "a222v"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "y453f",
          "dataType": "character",
          "sensitive": false,
          "description": "y453f"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "e484k",
          "dataType": "character",
          "sensitive": false,
          "description": "e484k"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "n501y",
          "dataType": "character",
          "sensitive": false,
          "description": "n501y"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "t1001i",
          "dataType": "character",
          "sensitive": false,
          "description": "t1001i"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "p681h",
          "dataType": "character",
          "sensitive": false,
          "description": "p681h"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "q27stop",
          "dataType": "character",
          "sensitive": false,
          "description": "q27stop"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "del_1605_3",
          "dataType": "character",
          "sensitive": false,
          "description": "del_1605_3"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "del_21765_6",
          "dataType": "character",
          "sensitive": false,
          "description": "del_21765_6"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "epcc_date_received",
          "dataType": "Date",
          "sensitive": false,
          "description": "epcc_date_received"
        }
      ],
      "description": "COG-UK Metadata File"
    },
    {
      "name": "UK SARS-CoV-2 viral sequencing data (COG-UK data)-Lineage/Variant Data-Scotland",
      "columns": [
        {
          "name": "epcc_date_inserted",
          "dataType": "Date Time",
          "sensitive": false,
          "description": "epcc_date_inserted"
        }
      ],
      "description": "COG-UK Metadata File"
    }
  ]
}

Copied to clipboard

Accessing data

Researcher Access Service

Work and impact

Case studies

Engage and learn

Data explainers

About RDS

Business plan 2025-26