COVID-19 Hospitalisation in England Surveillance System (CHESS) Dataset#
1. Summary#
The information below is retrieved from the Health Data Gateway API developed by NHS England, with additional fields added by UK LLC (indicated by italics). This dataset is now called the Severe Acute Respiratory Infection (SARI-WATCH) surveillance system dataset.
# define target dataset to document
schema = 'nhsd'
table = 'CHESS'
version = 'v0002'
# import functions from script helper
import sys
script_fp = "../../../../scripts/"
sys.path.insert(0, script_fp)
from data_doc_helper import DocHelper
# create instance
document = DocHelper(schema, table, version, script_fp)
# markdown/code hybrid cell module requirement
from IPython.display import display, Markdown
# get api data
dataset = document.get_api_data()
display(Markdown("**NHS England title of dataset:** "+dataset['datasetfields']['metadataquality']['title']))
display(Markdown("***Dataset name in UK LLC TRE:*** *nhsd.CHESS*"))
display(Markdown("**Short abstract:** "+dataset['datasetfields']['abstract']))
display(Markdown("***Extended abstract:*** *Formerly known as the COVID-19 Hospitalisation in England Surveillance System (CHESS) dataset, UK Health Security Agency's (UKHSA) Severe Acute Respiratory Infection (SARI-WATCH) surveillance system dataset records demographic, risk factor, treatment and outcome information for patients admitted to hospital in England with a confirmed COVID-19 diagnosis. This includes people admitted to intensive care or high dependency units.*"))
display(Markdown("**Geographical coverage:** "+dataset['datasetfields']['geographicCoverage'][0]))
display(Markdown("**Temporal coverage:** "+dataset['datasetfields']['datasetStartDate']))
display(Markdown("***Data available in UK LLC TRE from:*** *12/03/2020 to 01/10/2022*"))
display(Markdown("**Typical age range:** "+dataset['datasetfields']['ageBand']))
display(Markdown("**Collection situation:** "+dataset['datasetv2']['provenance']['origin']['collectionSituation'][0]))
display(Markdown("**Purpose:** "+dataset['datasetv2']['provenance']['origin']['purpose'][0]))
display(Markdown("**Source:** "+dataset['datasetv2']['provenance']['origin']['source'][0]))
display(Markdown("**Pathway:** "+dataset['datasetv2']['coverage']['pathway']))
display(Markdown("***Information collected:*** *Demographic information, risk factor, treatment and outcome information for patients admitted to hospital with a confirmed COVID-19 diagnosis. This includes people admitted to intensive care or high dependency units.*"))
display(Markdown("***Structure of dataset:*** *Each line represents one participant.*"))
display(Markdown("***Update frequency in UK LLC TRE:*** *N/A - dataset retired on 01/10/2022*"))
display(Markdown("***Dataset versions in UK LLC TRE:*** *TBC*"))
display(Markdown("***Data quality issues:*** *TBC*"))
display(Markdown("***Restrictions to data usage***: *Research must be related to COVID-19 and be for medical purposes only (medical research) as defined in the NHS Act 2006: [https://www.legislation.gov.uk/ukpga/2006/41/part/13/crossheading/patient-information](https://www.legislation.gov.uk/ukpga/2006/41/part/13/crossheading/patient-information)*"))
display(Markdown("***Further information:*** *[https://digital.nhs.uk/about-nhs-digital/corporate-information-and-documents/directions-and-data-provision-notices/data-provision-notices-dpns/sgss-and-sari-watch-data](https://digital.nhs.uk/about-nhs-digital/corporate-information-and-documents/directions-and-data-provision-notices/data-provision-notices-dpns/sgss-and-sari-watch-data)*"))
NHS England title of dataset: COVID-19 SARI-Watch (formerly CHESS)
Dataset name in UK LLC TRE: nhsd.CHESS
Short abstract: The COVID-19 SARI-Watch data set (formerly CHESS) relates to demographic, risk factor, treatment, and outcome information for patients admitted to hospital with a confirmed COVID-19 diagnosis, as recorded in the COVID-19 SARI-Watch surveillance system.
Extended abstract: Formerly known as the COVID-19 Hospitalisation in England Surveillance System (CHESS) dataset, UK Health Security Agency’s (UKHSA) Severe Acute Respiratory Infection (SARI-WATCH) surveillance system dataset records demographic, risk factor, treatment and outcome information for patients admitted to hospital in England with a confirmed COVID-19 diagnosis. This includes people admitted to intensive care or high dependency units.
Geographical coverage: https://www.geonames.org/6269131/england.html
Temporal coverage: 2020-03-12
Data available in UK LLC TRE from: 12/03/2020 to 01/10/2022
Typical age range: 0-150
Collection situation: IN-PATIENTS
Purpose: STUDY
Source: EPR
Pathway: Not Applicable
Information collected: Demographic information, risk factor, treatment and outcome information for patients admitted to hospital with a confirmed COVID-19 diagnosis. This includes people admitted to intensive care or high dependency units.
Structure of dataset: Each line represents one participant.
Update frequency in UK LLC TRE: N/A - dataset retired on 01/10/2022
Dataset versions in UK LLC TRE: TBC
Data quality issues: TBC
Restrictions to data usage: Research must be related to COVID-19 and be for medical purposes only (medical research) as defined in the NHS Act 2006: https://www.legislation.gov.uk/ukpga/2006/41/part/13/crossheading/patient-information
Further information: https://digital.nhs.uk/about-nhs-digital/corporate-information-and-documents/directions-and-data-provision-notices/data-provision-notices-dpns/sgss-and-sari-watch-data
2. Metrics#
The tables below summarise the CHESS dataset in the UK LLC TRE.
Table 1 The number of participants from each LPS that are represented in the CHESS dataset in the UK LLC TRE
(Note: numbers relate to the most recent extract of NHS England data. Numbers <10 are not included in the total)
gb_cohort = document.get_cohort_count()
print(gb_cohort.to_markdown(index=False, tablefmt="fancy_grid"))
╒════════════════╤═════════╕
│ cohort │ count │
╞════════════════╪═════════╡
│ ALSPAC │ 0 │
├────────────────┼─────────┤
│ BCS70 │ 11 │
├────────────────┼─────────┤
│ BIB │ <10 │
├────────────────┼─────────┤
│ ELSA │ 24 │
├────────────────┼─────────┤
│ EPICN │ <10 │
├────────────────┼─────────┤
│ EXCEED │ <10 │
├────────────────┼─────────┤
│ FENLAND │ 14 │
├────────────────┼─────────┤
│ GLAD │ 59 │
├────────────────┼─────────┤
│ MCS │ 19 │
├────────────────┼─────────┤
│ NCDS58 │ 11 │
├────────────────┼─────────┤
│ NEXTSTEP │ <10 │
├────────────────┼─────────┤
│ NIHRBIO_COPING │ 11 │
├────────────────┼─────────┤
│ NSHD46 │ 13 │
├────────────────┼─────────┤
│ TEDS │ 0 │
├────────────────┼─────────┤
│ TRACKC19 │ <10 │
├────────────────┼─────────┤
│ TWINSUK │ 25 │
├────────────────┼─────────┤
│ UKHLS │ <10 │
├────────────────┼─────────┤
│ total │ 187 │
╘════════════════╧═════════╛
3. Helpful syntax#
Below we will include syntax that may be helpful to other researchers in the UK LLC TRE. For longer scripts, we will include a snippet of the code plus a link to Git where you can find the full script.