National Pathology Exchange (NPEX) 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 also known as the Covid-19 UK Non-hospital Antigen Testing Results dataset.
# define target dataset to document
schema = 'nhsd'
table = 'NPEX'
version = 'v0003'
# 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']['datautility']['title']))
display(Markdown("***Dataset name in UK LLC TRE:*** *nhsd.NPEX*"))
display(Markdown("**Short abstract:** "+dataset['datasetfields']['abstract']))
display(Markdown("***Extended abstract:*** *Also known as the Covid-19 UK Non-hospital Antigen Testing Results dataset, NPEX reflects swab testing undertaken by the wider community at drive through test centres, walk in centres, home kits returned by post, care homes, etc. (i.e. Pillar 2). The dataset is UK wide and includes demographic and diagnostic information. For a full list of variables see the [NHS England Metadata dashboard.](https://digital.nhs.uk/services/data-access-request-service-dars/dars-products-and-services/metadata-dashboard)*"))
display(Markdown("**Geographical coverage:** "+dataset['datasetfields']['geographicCoverage'][0]))
display(Markdown("**Temporal coverage:** "+dataset['datasetfields']['datasetStartDate']))
display(Markdown("***Data available in UK LLC TRE from:*** *17/04/2020 onwards*"))
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 and diagnostic information*."))
display(Markdown("***Structure of dataset:*** *Each line represents one participant.*"))
display(Markdown("***Update frequency in UK LLC TRE:*** *Quarterly*"))
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/services/data-access-request-service-dars/dars-products-and-services/data-set-catalogue/covid-19-uk-non-hospital-antigen-testing-results-pillar-2](https://digital.nhs.uk/services/data-access-request-service-dars/dars-products-and-services/data-set-catalogue/covid-19-uk-non-hospital-antigen-testing-results-pillar-2)*"))
NHS England title of dataset: Covid-19 UK Non-hospital Antigen Testing Results
Dataset name in UK LLC TRE: nhsd.NPEX
Short abstract: COVID-19 UK Non-hospital Antigen Testing Results (Pillar 2) data is required by NHS Digital to support COVID-19 requests for linkage, analysis and dissemination.
Extended abstract: Also known as the Covid-19 UK Non-hospital Antigen Testing Results dataset, NPEX reflects swab testing undertaken by the wider community at drive through test centres, walk in centres, home kits returned by post, care homes, etc. (i.e. Pillar 2). The dataset is UK wide and includes demographic and diagnostic information. For a full list of variables see the NHS England Metadata dashboard.
Geographical coverage: United Kingdom,England
Temporal coverage: 20/04/2020
Data available in UK LLC TRE from: 17/04/2020 onwards
Typical age range: 0-150
Collection situation: IN-PATIENTS
Purpose: CARE
Source: LIMS
Pathway: NOT APPLICABLE
Information collected: Demographic and diagnostic information.
Structure of dataset: Each line represents one participant.
Update frequency in UK LLC TRE: Quarterly
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/services/data-access-request-service-dars/dars-products-and-services/data-set-catalogue/covid-19-uk-non-hospital-antigen-testing-results-pillar-2
2. Metrics#
The tables below summarise the NPEX dataset in the UK LLC TRE.
Table 1 The number of participants from each LPS that are represented in the NPEX dataset in the UK LLC TRE
Note: numbers relate to the most recent extract of NHS England data)
gb_cohort = document.get_cohort_count()
print(gb_cohort.to_markdown(index=False, tablefmt="fancy_grid"))
╒════════════════╤═════════╕
│ cohort │ count │
╞════════════════╪═════════╡
│ ALSPAC │ 5141 │
├────────────────┼─────────┤
│ BCS70 │ 4501 │
├────────────────┼─────────┤
│ BIB │ 20239 │
├────────────────┼─────────┤
│ ELSA │ 3977 │
├────────────────┼─────────┤
│ EPICN │ 7109 │
├────────────────┼─────────┤
│ EXCEED │ 6899 │
├────────────────┼─────────┤
│ FENLAND │ 7558 │
├────────────────┼─────────┤
│ GLAD │ 54548 │
├────────────────┼─────────┤
│ MCS │ 14289 │
├────────────────┼─────────┤
│ NCDS58 │ 4067 │
├────────────────┼─────────┤
│ NEXTSTEP │ 4302 │
├────────────────┼─────────┤
│ NIHRBIO_COPING │ 13893 │
├────────────────┼─────────┤
│ NSHD46 │ 1098 │
├────────────────┼─────────┤
│ TEDS │ 6914 │
├────────────────┼─────────┤
│ TRACKC19 │ 12308 │
├────────────────┼─────────┤
│ TWINSUK │ 8823 │
├────────────────┼─────────┤
│ UKHLS │ 5352 │
├────────────────┼─────────┤
│ total │ 181018 │
╘════════════════╧═════════╛
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.