From 8d265a1d047a0f57449e7c913281c5c3f48727fe Mon Sep 17 00:00:00 2001 From: Thomas O'Dwyer Date: Tue, 20 Jan 2026 16:26:11 +0000 Subject: [PATCH 1/3] Update data sources for new direction --- docs/data-sources/index.md | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/docs/data-sources/index.md b/docs/data-sources/index.md index 7aef4f8cc..fb3c2b45f 100644 --- a/docs/data-sources/index.md +++ b/docs/data-sources/index.md @@ -1,3 +1,21 @@ # Data Sources -{{ build_toc(navigation, page) }} +- [Overview](./intro.md) + +## Datasets available for all research under the New Direction + +- [SystmOne primary care (General Practice coded events)](./systmone.md) +- [Hospital admissions (hospital spells, outpatients and A&E)](./apc.md) +- [ONS Registered Deaths](./onsdeaths.md) + +## Other datasets under the COVID Direction + +- [EMIS primary care](./emis.md) +- [Covid-19 test results](./sgsscovid.md) +- [Covid-19 therapeutics](./therapeutics.md) +- [Emergency attendances](./ecds.md) +- [High Cost Drugs](./hcd.md) +- [In-hospital deaths (covid-19 only)](./cpns.md) +- [Intensive care admissions (covid-19 only)](./icnarc.md) +- [International Severe Acute Respiratory and emerging Infection Consortium](./isaric.md) +- [UK Renal Registry](./ukrr.md) From 7c32dc4c3c67a7bdf1a8df061f86310b2bbce078 Mon Sep 17 00:00:00 2001 From: Thomas O'Dwyer Date: Tue, 20 Jan 2026 16:59:04 +0000 Subject: [PATCH 2/3] Update data sources pages formatting Using definition lists for metadata and Prettier for formatting --- docs/data-sources/apc.md | 121 +++++++++++++++++------------- docs/data-sources/cpns.md | 32 +++++--- docs/data-sources/ecds.md | 40 ++++++---- docs/data-sources/emis.md | 7 +- docs/data-sources/hcd.md | 31 ++++---- docs/data-sources/icnarc.md | 41 ++++++---- docs/data-sources/intro.md | 2 +- docs/data-sources/onsdeaths.md | 41 +++++++--- docs/data-sources/sgsscovid.md | 36 +++++---- docs/data-sources/systmone.md | 47 ++++++------ docs/data-sources/therapeutics.md | 53 +++++++++---- docs/data-sources/ukrr.md | 22 ++++-- mkdocs.yml | 1 + 13 files changed, 289 insertions(+), 185 deletions(-) diff --git a/docs/data-sources/apc.md b/docs/data-sources/apc.md index c11f349c7..df6113f5d 100644 --- a/docs/data-sources/apc.md +++ b/docs/data-sources/apc.md @@ -3,26 +3,37 @@ Admitted Patient Care Spells (APCS) is part of Hospital Episode Statistics (HES) ## Metadata -* **Data provider** NHS England. -* **Participation / Coverage** In-hospital patient admissions in NHS Trusts in England. -* **Available from** Data are available from early 2016. -* **Update frequency in OpenSAFELY** Approximately monthly. -* **Delay between event occurring and event appearing in OpenSAFELY** Approximately 1-2 months. -* **Collected information** Admission and discharge dates; routes of admission; reason for admission; diagnoses; treatments; discharge destination. +**Data provider** +: NHS England. +**Participation / Coverage** +: In-hospital patient admissions in NHS Trusts in England. + +**Available from** +: Data are available from early 2016. + +**Update frequency in OpenSAFELY** +: Approximately monthly. + +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 1-2 months. + +**Collected information** +: Admission and discharge dates; routes of admission; reason for admission; diagnoses; treatments; discharge destination. ## Basic Background Each row is a in-hospital spell. In-hospital episodes cannot be queried. -* An **episode** is a period of continuous care under a single responsible consultant. -* A **spell** is a period of continuous care within a single trust. +- An **episode** is a period of continuous care under a single responsible consultant. +- A **spell** is a period of continuous care within a single trust. Essentially, a spell is a collection of episodes (often just one episode) denoting the entirety of a patient's stay in hospital from admission to discharge or death. An episode denotes time within a spell spent under the responsibility of a single consultant. So for example if within your hospital stay you are transferred from a medical to surgical ward, or transferred to another site (within the same trust), there will be at least two episodes within your spell. The dataset does not include any patients who have not been discharged (i.e., patients who have an incomplete spell) at the data extraction date. In other words, the data will be missing admissions of the patients with the longest stay for the most recent admissions. ### \* Notes on transfers: + - Sometimes it is desirable to exclude patients admitted via transfer from another provider, e.g. if we are looking for readmissions we probably want to exclude them because it was not the original admission date of the readmission. - The post-transfer spell may have additional diagnoses or procedures of interest so it is often useful to include them. - Transfers may occasionally come from private hospitals where a patient's condition worsened to require e.g. intensive care; if the initial spell was not NHS funded we would probably not have the original spell in our data. @@ -30,63 +41,65 @@ The dataset does not include any patients who have not been discharged (i.e., pa ## Reference tables ### Admission method reference table -Codes | Admission method --- | -- -11, 12, 13 | Elective (planned/booked/waiting list) -21 | Emergency Admission: from A&E | usually include -2A | Emergency Admission: from A&E of another provider -22, 23, 24, 25, 2D | Emergency Admission: other sources (e.g. GP, MH crisis team) -28 | Emergency Admission: Other - NB can include transfers and births -2B | Transfer (emergency) -81 | Transfer (non-emergency) -2C, 82, 83 | Birth of baby (in hospital or e.g. at home) -31, 32 | Maternity Admission: Mother admitted ante or post partum + +| Codes | Admission method | | +| ------------------ | ---------------------------------------------------------------- | --------------- | +| 11, 12, 13 | Elective (planned/booked/waiting list) | | +| 21 | Emergency Admission: from A&E | usually include | +| 2A | Emergency Admission: from A&E of another provider | | +| 22, 23, 24, 25, 2D | Emergency Admission: other sources (e.g. GP, MH crisis team) | | +| 28 | Emergency Admission: Other - NB can include transfers and births | | +| 2B | Transfer (emergency) | | +| 81 | Transfer (non-emergency) | | +| 2C, 82, 83 | Birth of baby (in hospital or e.g. at home) | | +| 31, 32 | Maternity Admission: Mother admitted ante or post partum | | ### Source of admission reference table -code | Source of admission --- | -- -19 | Usual place of residence or no fixed abode (but should exclude care homes) -29 | Temporary place of residence (e.g. hotel, school) -54, 65, 85, 88 | Care Home / hospice -51 | NHS other Hospital Provider - ordinary (physical care) ward or A&E -49, 52, 53 | NHS other Hospital Provider - psychiatric accommodation, maternity ward/neonates or MH/LD ward -39, 40, 41, 42, 66 | Other (Penal establishment, Court, or Police Station / Police Custody Suite, foster care) -79 | Babies born in or on the way to hospital -87 | Non NHS run hospital -98, 99 | Default/unknown + +| code | Source of admission | +| ------------------ | ---------------------------------------------------------------------------------------------- | +| 19 | Usual place of residence or no fixed abode (but should exclude care homes) | +| 29 | Temporary place of residence (e.g. hotel, school) | +| 54, 65, 85, 88 | Care Home / hospice | +| 51 | NHS other Hospital Provider - ordinary (physical care) ward or A&E | +| 49, 52, 53 | NHS other Hospital Provider - psychiatric accommodation, maternity ward/neonates or MH/LD ward | +| 39, 40, 41, 42, 66 | Other (Penal establishment, Court, or Police Station / Police Custody Suite, foster care) | +| 79 | Babies born in or on the way to hospital | +| 87 | Non NHS run hospital | +| 98, 99 | Default/unknown | ### Patient classification reference table -code | patient classification --- | -- -1 | Ordinary admission (all emergency admissions and elective admissions expected to last at least one night) -2 | Day case admission (patient admitted electively, not expected to stay overnight and who returns home on the same day as scheduled. If discharge does not occur same day as planned, this should be counted as an ordinary admission) -3, 4 | Regular day or night admission (part of a planned series of regular admissions for an on-going regime of broadly similar treatment. If the admission lasts 24 hours or more, such an admission should be classified as an ordinary admission) -5 | Mother and baby using delivery facilities only +| code | patient classification | +| ---- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 1 | Ordinary admission (all emergency admissions and elective admissions expected to last at least one night) | +| 2 | Day case admission (patient admitted electively, not expected to stay overnight and who returns home on the same day as scheduled. If discharge does not occur same day as planned, this should be counted as an ordinary admission) | +| 3, 4 | Regular day or night admission (part of a planned series of regular admissions for an on-going regime of broadly similar treatment. If the admission lasts 24 hours or more, such an admission should be classified as an ordinary admission) | +| 5 | Mother and baby using delivery facilities only | ### Discharge destination reference table -Code | Description --- | -- -19 | Usual place of residence unless listed below. It includes 'no fixed abode' but excludes care homes. -29 | Temporary place of residence (includes hotel, residential Educational Establishment) -51, 52 | Transfer: NHS other Hospital Provider - general ward or maternity/ neonates -30, 49, 50, 53 | Transfer (other NHS):, mentally ill / Learning Disabilities, psychiatric units -48, 84, 87 | Transfer: Non-NHS run hospital or medium secure unit, Scotland high-secure unit -37, 38, 66 | Other: Court, Penal establishment, police station, foster care -54, 65, 85, 88 | Hospice / Care Home -79 | Not applicable - PATIENT died or stillbirth +| Code | Description | +| -------------- | --------------------------------------------------------------------------------------------------- | +| 19 | Usual place of residence unless listed below. It includes 'no fixed abode' but excludes care homes. | +| 29 | Temporary place of residence (includes hotel, residential Educational Establishment) | +| 51, 52 | Transfer: NHS other Hospital Provider - general ward or maternity/ neonates | +| 30, 49, 50, 53 | Transfer (other NHS):, mentally ill / Learning Disabilities, psychiatric units | +| 48, 84, 87 | Transfer: Non-NHS run hospital or medium secure unit, Scotland high-secure unit | +| 37, 38, 66 | Other: Court, Penal establishment, police station, foster care | +| 54, 65, 85, 88 | Hospice / Care Home | +| 79 | Not applicable - PATIENT died or stillbirth | #### Reference -[Link to lookup table](https://datadictionary.nhs.uk/attributes/discharge_destination.html?hl=discharge%2Cdestination) +[Link to lookup table](https://datadictionary.nhs.uk/attributes/discharge_destination.html?hl=discharge%2Cdestination) ## More information -* [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) -* [NHS Digital SUS site](https://digital.nhs.uk/services/secondary-uses-service-sus/secondary-uses-services-sus-guidance) -* [NHS Digital HES site](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/hospital-episode-statistics) -* [Hospital APC Activity reports](https://digital.nhs.uk/data-and-information/publications/statistical/hospital-admitted-patient-care-activity) -* [NHS Digital APC data dictionary](https://datadictionary.nhs.uk/data_sets/cds_v6-2/cds_v6-2_type_130_-_admitted_patient_care_-_finished_general_episode_cds.html) -* [Data resource profile: Hospital Episode Statistics Admitted Patient Care (HES APC)](https://doi.org/10.1093/ije/dyx015) -* [CLOSER Understanding Hospital Episode Statistics](https://www.closer.ac.uk/wp-content/uploads/CLOSER-resource-understanding-hospital-episode-statistics-2018.pdf) +- [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) +- [NHS Digital SUS site](https://digital.nhs.uk/services/secondary-uses-service-sus/secondary-uses-services-sus-guidance) +- [NHS Digital HES site](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/hospital-episode-statistics) +- [Hospital APC Activity reports](https://digital.nhs.uk/data-and-information/publications/statistical/hospital-admitted-patient-care-activity) +- [NHS Digital APC data dictionary](https://datadictionary.nhs.uk/data_sets/cds_v6-2/cds_v6-2_type_130_-_admitted_patient_care_-_finished_general_episode_cds.html) +- [Data resource profile: Hospital Episode Statistics Admitted Patient Care (HES APC)](https://doi.org/10.1093/ije/dyx015) +- [CLOSER Understanding Hospital Episode Statistics](https://www.closer.ac.uk/wp-content/uploads/CLOSER-resource-understanding-hospital-episode-statistics-2018.pdf) diff --git a/docs/data-sources/cpns.md b/docs/data-sources/cpns.md index bac1922d3..b71c7c155 100644 --- a/docs/data-sources/cpns.md +++ b/docs/data-sources/cpns.md @@ -3,15 +3,27 @@ Initially this was lab-confirmed covid deaths only, but also includes suspected ## Metadata -* **Data provider** NHS England. -* **Participation / Coverage** In-hospital covid-related deaths in England. -* **Update frequency in OpenSAFELY** Weekly. -* **Delay between event occurring and event appearing in OpenSAFELY** Within 2 weeks. -* **Available from** 24/03/2020 onwards (all test-positive deaths); 28/04/2020 onwards (test-positive and covid documented as underlying cause). -* **Collected information** Admission, test, result, and death dates; hospital and department of death; basic demographics. +**Data provider** +: NHS England. + +**Participation / Coverage** +: In-hospital covid-related deaths in England. + +**Update frequency in OpenSAFELY** +: Weekly. + +**Delay between event occurring and event appearing in OpenSAFELY** +: Within 2 weeks. + +**Available from** +: 24/03/2020 onwards (all test-positive deaths); 28/04/2020 onwards (test-positive and covid documented as underlying cause). + +**Collected information** +: Admission, test, result, and death dates; hospital and department of death; basic demographics. ## More information -* [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) -* [Press release from Arden&GEM](https://www.ardengemcsu.nhs.uk/showcase/news-events/news-events/supporting-providers-to-record-covid-19-patient-notifications/) -* [Letter from NHSE to Trust chief execs regarding changes to data collection](https://www.england.nhs.uk/coronavirus/wp-content/uploads/sites/52/2020/04/C0389-update-to-cpns-reporting-letter-27-april-2020.pdf) -* [Technical summary on data series on deaths in people with COVID-19](https://www.gov.uk/government/publications/phe-data-series-on-deaths-in-people-with-covid-19-technical-summary) + +- [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) +- [Press release from Arden&GEM](https://www.ardengemcsu.nhs.uk/showcase/news-events/news-events/supporting-providers-to-record-covid-19-patient-notifications/) +- [Letter from NHSE to Trust chief execs regarding changes to data collection](https://www.england.nhs.uk/coronavirus/wp-content/uploads/sites/52/2020/04/C0389-update-to-cpns-reporting-letter-27-april-2020.pdf) +- [Technical summary on data series on deaths in people with COVID-19](https://www.gov.uk/government/publications/phe-data-series-on-deaths-in-people-with-covid-19-technical-summary) diff --git a/docs/data-sources/ecds.md b/docs/data-sources/ecds.md index 3fa41dfb2..ce1cb5735 100644 --- a/docs/data-sources/ecds.md +++ b/docs/data-sources/ecds.md @@ -3,21 +3,33 @@ ECDS is part of Hospital Episode Statistics (HES) and is provided to OpenSAFELY ## Metadata -* **Data provider** NHS England. -* **Participation / Coverage** Emergency Department attendances in NHS Trusts in England. -* **Available from** Data are available from late 2017; however, ECDS was in a pilot phase until 2020 and data are incomplete prior to approximately early 2019. -* **Update frequency in OpenSAFELY** Approximately monthly. -* **Delay between event occurring and event appearing in OpenSAFELY** * Approximately 1-2 months. -* **Collected information** Attendance, admission and discharge dates; locations; presenting complaints; diagnoses. +**Data provider:** +: NHS England. + +**Participation / Coverage:** +: Emergency Department attendances in NHS Trusts in England. + +**Available from:** +: Data are available from late 2017; however, ECDS was in a pilot phase until 2020 and data are incomplete prior to approximately early 2019. + +**Update frequency in OpenSAFELY** +: Approximately monthly. + +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 1-2 months. + +**Collected information** +: Attendance, admission and discharge dates; locations; presenting complaints; diagnoses. Diagnoses and discharge destinations are coded using SNOMED CT. ## More information -* [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) -* [NHS Digital ECDS site](https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-sets/emergency-care-data-set-ecds) -* [NHS Digital SUS site](https://digital.nhs.uk/services/secondary-uses-service-sus/secondary-uses-services-sus-guidance) -* [NHS Digital HES site](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/hospital-episode-statistics) -* [NHS Digital ECDS data dictionary](https://www.datadictionary.nhs.uk/data_sets/cds_v6-2/cds_v6-2-3_type_011_-_emergency_care_cds.html) -* [NHS Digital ECDS Information Standard](https://digital.nhs.uk/data-and-information/information-standards/information-standards-and-data-collections-including-extractions/publications-and-notifications/standards-and-collections/dcb0092-2062-commissioning-data-sets-emergency-care-data-set ) -* [NHS Digital ECDS Technical Output Specification](https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-sets/emergency-care-data-set-ecds/ecds-latest-update) -* [ECDS Data Quality Dashboards](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/emergency-care-data-set-ecds-data-quality ) + +- [Notebook showing breakdown of ethnicity codes](https://github.com/opensafely/rapid-reports/blob/master/notebooks/ethnicity-codes.ipynb) - (private, pending review & publication) +- [NHS Digital ECDS site](https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-sets/emergency-care-data-set-ecds) +- [NHS Digital SUS site](https://digital.nhs.uk/services/secondary-uses-service-sus/secondary-uses-services-sus-guidance) +- [NHS Digital HES site](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/hospital-episode-statistics) +- [NHS Digital ECDS data dictionary](https://www.datadictionary.nhs.uk/data_sets/cds_v6-2/cds_v6-2-3_type_011_-_emergency_care_cds.html) +- [NHS Digital ECDS Information Standard](https://digital.nhs.uk/data-and-information/information-standards/information-standards-and-data-collections-including-extractions/publications-and-notifications/standards-and-collections/dcb0092-2062-commissioning-data-sets-emergency-care-data-set) +- [NHS Digital ECDS Technical Output Specification](https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-sets/emergency-care-data-set-ecds/ecds-latest-update) +- [ECDS Data Quality Dashboards](https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/emergency-care-data-set-ecds-data-quality) diff --git a/docs/data-sources/emis.md b/docs/data-sources/emis.md index 70fdc7e71..4cc926e1f 100644 --- a/docs/data-sources/emis.md +++ b/docs/data-sources/emis.md @@ -1,10 +1,7 @@ !!! warning - Research access to the backend provided by EMIS is temporarily unavailable, - pending funding arrangements between NHS England and EMIS. - When funding has been secured, - we will publish a timeline for gradually reopening access. + Research access to the backend provided by EMIS is temporarily unavailable, pending funding arrangements between NHS England and EMIS. When funding has been secured, we will publish a timeline for gradually reopening access. ## OpenSAFELY-EMIS database builds When EMIS receive data from external data sources (eg ONS), records are appended to the -relevant tables, not updated. The relevant tables have an `upload_date` column, and to get the latest data, we have to query for on `upload_date`. +relevant tables, not updated. The relevant tables have an `upload_date` column, and to get the latest data, we have to query for on `upload_date`. diff --git a/docs/data-sources/hcd.md b/docs/data-sources/hcd.md index 4580b2eb3..ce8aa3e55 100644 --- a/docs/data-sources/hcd.md +++ b/docs/data-sources/hcd.md @@ -1,17 +1,25 @@ -The High Cost Drugs (HCD) data is a dataset containing specialist medicines prescribed by hospitals to patients for the management of long term conditions. +The High Cost Drugs (HCD) data is a dataset containing specialist medicines prescribed by hospitals to patients for the management of long term conditions. ## Metadata -* **Data provider** North East Commissioning Support Unit (NECS) with approvals from NHS Digital. -* **Participation / Coverage** Hospital prescribing of [high cost drugs](https://www.england.nhs.uk/publication/nhs-england-drugs-list/) across all 135 CCGs nationally. -* **Update frequency in OpenSAFELY** Data covering April 2018 to March 2020 is currently available in OpenSAFELY, with no updates planned (see discussion section of [paper](https://wellcomeopenresearch.org/articles/6-360) for our proposal). -* **Delay between event occurring and event appearing in OpenSAFELY** NA - currently a one off extract. -* **Collected information** Patient characteristics; clinical indications; medicine prescribed. +**Data provider** +: North East Commissioning Support Unit (NECS) with approvals from NHS Digital. +**Participation / Coverage** +: Hospital prescribing of [high cost drugs](https://www.england.nhs.uk/publication/nhs-england-drugs-list/) across all 135 CCGs nationally. + +**Update frequency in OpenSAFELY** +: Data covering April 2018 to March 2020 is currently available in OpenSAFELY, with no updates planned (see discussion section of [paper](https://wellcomeopenresearch.org/articles/6-360) for our proposal). + +**Delay between event occurring and event appearing in OpenSAFELY** +: NA - currently a one off extract. + +**Collected information** +: Patient characteristics; clinical indications; medicine prescribed. ## Basic Background -Hospitals in England supply medicines to patients either directly or through “homecare” providers who deliver medicines to a patient's home. The majority of medicines are funded through overall hospital contracts, included in tariffs; however, for certain HCDs, hospitals are required to provide a submission for each patient to the relevant commissioner, either NHSE or one of 135 local CCGs, in order to receive payment. +Hospitals in England supply medicines to patients either directly or through “homecare” providers who deliver medicines to a patient's home. The majority of medicines are funded through overall hospital contracts, included in tariffs; however, for certain HCDs, hospitals are required to provide a submission for each patient to the relevant commissioner, either NHSE or one of 135 local CCGs, in order to receive payment. The majority of submissions relate to a prescription of a HCD, although some submissions relate to associated services (i.e. home care delivery charges). There is a [national list](https://www.england.nhs.uk/publication/nhs-england-drugs-list/) of the medicines that are funded by NHSE and locally agreed lists for each CCG. These patient-level submissions are processed by intermediate organisations, Commissioning Support Units (CSUs), to support financial payments and associated activities like summary reporting. This dataset contains data collated from all 135 CCGs to create a single comprehensive dataset. @@ -19,14 +27,9 @@ The HCD dataset is a patient-level dataset and includes variables on patient cha A [paper describing](https://wellcomeopenresearch.org/articles/6-360) the HCD dataset was published in December 2021. - ## More information -* [A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report](https://wellcomeopenresearch.org/articles/6-360) -* National Data Dictionary: [Drugs Patient Level Contract Monitoring Data Set](https://www.datadictionary.nhs.uk/data_sets/supporting_data_sets/drugs_patient_level_contract_monitoring_data_set.html?hl=drugs%2Cpatient%2Clevel%2Ccontract%2Cmonitoring%2Cdata%2Cset) - +- [A comprehensive high cost drugs dataset from the NHS in England - An OpenSAFELY-TPP Short Data Report](https://wellcomeopenresearch.org/articles/6-360) +- National Data Dictionary: [Drugs Patient Level Contract Monitoring Data Set](https://www.datadictionary.nhs.uk/data_sets/supporting_data_sets/drugs_patient_level_contract_monitoring_data_set.html?hl=drugs%2Cpatient%2Clevel%2Ccontract%2Cmonitoring%2Cdata%2Cset) --8<-- "includes/glossary.md" - - - diff --git a/docs/data-sources/icnarc.md b/docs/data-sources/icnarc.md index c86cdd9e7..c39fc308d 100644 --- a/docs/data-sources/icnarc.md +++ b/docs/data-sources/icnarc.md @@ -1,8 +1,7 @@ -The ICNARC-CMP dataset contains information on covid-related intensive care admissions in England. +The ICNARC-CMP dataset contains information on covid-related intensive care admissions in England. !!! warning - ICNARC data can only be used in collaboration with ICNARC researchers who must be involved in working on the study and writing it up. - Please contact your co-pilot, or if you have any questions. + ICNARC data can only be used in collaboration with ICNARC researchers who must be involved in working on the study and writing it up. Please contact your co-pilot, or if you have any questions. !!! warning Data from ICNARC were last imported on 21-Jan-2021, with no further imports currently planned. Alternative data on ICU admission can be gleaned from SUS (i.e. returning=days_in_critical_care). @@ -16,23 +15,39 @@ Currently only Covid-19 positive patients are provided by ICNARC. ## Metadata -* **Data provider** ICNARC -* **Participation / Coverage** Adult ICU/HDUs admissions in England, Wales, NI. +**Data provider** +: ICNARC + +**Participation / Coverage** +: Adult ICU/HDUs admissions in England, Wales, NI. Specialist units (eg neuro / cardiac) also participate. covid-19 admissions only -* **Provenance** ICUs and HDUs -* **Update frequency in OpenSAFELY** Approximately weekly. -* **Delay between event occurring and event appearing in OpenSAFELY** Approximately 1-2 weeks. -* **Collected information** Admission, discharge and transfer dates; reason for admission; clinical support/interventions; clinical findings + +**Provenance** +: ICUs and HDUs + +**Update frequency in OpenSAFELY** +: Approximately weekly. + +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 1-2 weeks. + +**Collected information** +: Admission, discharge and transfer dates; reason for admission; clinical support/interventions; clinical findings ## More Information -[CMP resources]( https://www.icnarc.org/Our-Audit/Audits/Cmp/Resources) — this is comprehensive, and includes links to the data dictionary, CRF, data flows, and other useful resources. +[CMP resources](https://www.icnarc.org/Our-Audit/Audits/Cmp/Resources) — this is comprehensive, and includes links to the data dictionary, CRF, data flows, and other useful resources. ## Datasource-specific glossary -* **Advanced respiratory support** unclear, possibly non-intubated ventilation -* **Basic respiratory support** unclear, possibly intubated ventilation -* **Admission** these include _any_ admission to ICU even if the patient did not require critical care, for example due to bed pressures elsewhere in the hospital. +**Advanced respiratory support** +: unclear, possibly non-intubated ventilation + +**Basic respiratory support** +: unclear, possibly intubated ventilation + +**Admission** +: these include _any_ admission to ICU even if the patient did not require critical care, for example due to bed pressures elsewhere in the hospital. It may be useful to filter by severity, e.g., ventilated patients only. Similarly, potentially critically ill patients cared-for by ICU staff but who are admitted to a different unit will not be included in the CMP. Each admission is a row, so patients transferred to other units will appear in the dataset multiple times, even if it’s part of the same spell. diff --git a/docs/data-sources/intro.md b/docs/data-sources/intro.md index d0a05eec9..fb223f627 100644 --- a/docs/data-sources/intro.md +++ b/docs/data-sources/intro.md @@ -3,8 +3,8 @@ To learn about querying the data, refer to the [documentation on ehrQL](../ehrql View information on [available datasets](index.md). - ## What is primary care data? + The core patient-level data used within OpenSAFELY is based on electronic GP records that are collected and securely stored to facilitate patient management by healthcare providers. They capture symptoms, test results, diagnoses, prescriptions, onward referrals, demographic and social characteristics, and so on. Essentially, everything about a patient that is electronically recorded or accessed by GPs. GP records, or primary care records, can also be used for conducting health research, which is what OpenSAFELY was built for. We've made a video to help explain primary care data in more detail; essential viewing if you're new to this domain. diff --git a/docs/data-sources/onsdeaths.md b/docs/data-sources/onsdeaths.md index 55cfbc972..43ad19e2d 100644 --- a/docs/data-sources/onsdeaths.md +++ b/docs/data-sources/onsdeaths.md @@ -2,22 +2,39 @@ Date and cause of death based on information recorded when deaths are certified ## Metadata -* **Data provider** Office for National Statistics. -* **Participation / Coverage** Deaths occurring in England and Wales, including non-residents. -* **Provenance** General Register Office. -* **Update frequency in OpenSAFELY** Approximately weeekly. -* **Available from** deaths recorded from February 2019 onwards. -* **Delay between event occurring and event appearing in OpenSAFELY** Approximately 1-2 weeks. -* **Collected information** Date of death, causes of death, age, sex, place of death. +**Data provider** +: Office for National Statistics. + +**Participation / Coverage** +: Deaths occurring in England and Wales, including non-residents. + +**Provenance** +: General Register Office. + +**Update frequency in OpenSAFELY** +: Approximately weeekly. + +**Available from** +: deaths recorded from February 2019 onwards. + +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 1-2 weeks. + +**Collected information** +: Date of death, causes of death, age, sex, place of death. Causes of death are coded using ICD-10. ## More information -* [Information collected at death registration](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/methodologies/userguidetomortalitystatisticsjuly2017#information-collected-at-death-registration) -* [User guide to mortality statistics](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/methodologies/userguidetomortalitystatisticsjuly2017) -* [Metadata](https://www.ons.gov.uk/aboutus/transparencyandgovernance/freedomofinformationfoi/howdeathregistrationsarerecordedandstoredbyons) +- [Information collected at death registration](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/methodologies/userguidetomortalitystatisticsjuly2017#information-collected-at-death-registration) +- [User guide to mortality statistics](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/methodologies/userguidetomortalitystatisticsjuly2017) +- [Metadata](https://www.ons.gov.uk/aboutus/transparencyandgovernance/freedomofinformationfoi/howdeathregistrationsarerecordedandstoredbyons) ## Glossary -* **Underlying cause of death (icd10u)** A cause code that identifies the medical condition judged to be the underlying cause of death according to the rules of the _10th Revision of the International Classification of Diseases_. This field appears once for each cause coded routine and inquest death (deaths at age 28 days and over). This code is generally known as 'the cause of death' and is used in single cause tabulations and analyses. The death is assigned the ICD10U code on the basis of ICD-10 codes allocated to the death by the MICAR program. A coder may also manually assign these codes to a death record. -* **Primary / secondary cause of death** These are not concepts used in ONS cause of death data. There is the underlying cause, and then a list of up to 15 medical conditions (`ICD10001` to `ICD10015`, given as ICD-10 codes) mentioned on the death certificate. These codes are not ordered meaningfully. + +**Underlying cause of death (icd10u)** +: A cause code that identifies the medical condition judged to be the underlying cause of death according to the rules of the _10th Revision of the International Classification of Diseases_. This field appears once for each cause coded routine and inquest death (deaths at age 28 days and over). This code is generally known as 'the cause of death' and is used in single cause tabulations and analyses. The death is assigned the ICD10U code on the basis of ICD-10 codes allocated to the death by the MICAR program. A coder may also manually assign these codes to a death record. + +**Primary / secondary cause of death** +: These are not concepts used in ONS cause of death data. There is the underlying cause, and then a list of up to 15 medical conditions (`ICD10001` to `ICD10015`, given as ICD-10 codes) mentioned on the death certificate. These codes are not ordered meaningfully. diff --git a/docs/data-sources/sgsscovid.md b/docs/data-sources/sgsscovid.md index ee4683eaa..24812765c 100644 --- a/docs/data-sources/sgsscovid.md +++ b/docs/data-sources/sgsscovid.md @@ -1,22 +1,30 @@ -> The Second Generation Surveillance System (SGSS) is an application that stores and manages data on laboratory isolates and notifications, and is the preferred method for capturing routine laboratory surveillance data on infectious diseases and antimicrobial resistance from laboratories across England. -- [UKHSA Laboratory Reporting Guidelines, page 5](https://assets.publishing.service.gov.uk/media/66e2e0ba0d913026165c3d77/UKHSA_Laboratory_reporting_guidelines_May_2023.pdf#page=5) - +> The Second Generation Surveillance System (SGSS) is an application that stores and manages data on laboratory isolates and notifications, and is the preferred method for capturing routine laboratory surveillance data on infectious diseases and antimicrobial resistance from laboratories across England. -- [UKHSA Laboratory Reporting Guidelines, page 5](https://assets.publishing.service.gov.uk/media/66e2e0ba0d913026165c3d77/UKHSA_Laboratory_reporting_guidelines_May_2023.pdf#page=5) SGSS data currently available in OpenSAFELY is for SARS-COV-2 test results from the UK's Pillar 1 and Pillar 2 tests. Some SARS-CoV-2 testing info also flows directly into the primary care record from SGSS (see below). - ## Metadata +**Data provider** +: Public Health England + +**Participation / Coverage** +: Unclear, and varies over time + +**Provenance** +: PHE and NHS hospital testing labs -* **Data provider** Public Health England -* **Participation / Coverage** Unclear, and varies over time -* **Provenance** PHE and NHS hospital testing labs -* **Update frequency in OpenSAFELY** Approximately monthly -* **Delay between event occurring and event appearing in OpenSAFELY** Approximately 1-2 weeks. -* **Collected information** Earliest specimen date, lab report date, age, sex, county, test result, source ("pillar 2" or "other") +**Update frequency in OpenSAFELY** +: Approximately monthly +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 1-2 weeks. + +**Collected information** +: Earliest specimen date, lab report date, age, sex, county, test result, source ("pillar 2" or "other") ## Overview + SGSS contains information on patients receiving a swab test for SARS-CoV-2, from Pillar 1 (NHS and PHE labs) and Pillar 2 (commercial partners). It includes "earliest specimen date" (when the sample was taken); "lab report date" (when the result was uploaded to SGSS system); pillar 2 or "other"; result (pos/neg); some demographics. @@ -32,13 +40,11 @@ Other viruses/organisms may have a finite episode length, so that any tests occu SARS-CoV-2 test results from various sources are also coded [within SystmOne](systmone.md). - ## More information -* [Regarding lab-confirmed cases](https://coronavirus.data.gov.uk/about#total-and-daily-uk-cases) -* [National COVID-19 surveillance reports](https://www.gov.uk/government/publications/national-covid-19-surveillance-reports) -* [Testing methodology](https://www.gov.uk/government/publications/coronavirus-covid-19-testing-data-methodology/covid-19-testing-data-methodology-note) -* [Testing strategy](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/878121/coronavirus-covid-19-testing-strategy.pdf#page=8) - +- [Regarding lab-confirmed cases](https://coronavirus.data.gov.uk/about#total-and-daily-uk-cases) +- [National COVID-19 surveillance reports](https://www.gov.uk/government/publications/national-covid-19-surveillance-reports) +- [Testing methodology](https://www.gov.uk/government/publications/coronavirus-covid-19-testing-data-methodology/covid-19-testing-data-methodology-note) +- [Testing strategy](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/878121/coronavirus-covid-19-testing-strategy.pdf#page=8) --8<-- "includes/glossary.md" diff --git a/docs/data-sources/systmone.md b/docs/data-sources/systmone.md index ee7757af1..f109979eb 100644 --- a/docs/data-sources/systmone.md +++ b/docs/data-sources/systmone.md @@ -17,8 +17,7 @@ Medications are coded using DM+D codes, and are available in the `MedicationIssu The `Vaccination` table contains information on administered vaccinations, identified using either the target disease (e.g., influenza), or the vaccine product (e.g., Optaflu). !!! warning - Detailed information on onward referrals is not currently available. - A subset of referrals are recorded in the `CodedEvent` table but this data will be incomplete. + Detailed information on onward referrals is not currently available. A subset of referrals are recorded in the `CodedEvent` table but this data will be incomplete. Only coded or other structured data can be accessed in OpenSAFELY — we do not have access to free text data. @@ -26,9 +25,9 @@ Only coded or other structured data can be accessed in OpenSAFELY — we do SARS-CoV-2 test result data is incorporated into SystmOne and uses the following CTV3 codes: -* **Y20d1** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result positive_ -* **Y20d2** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result negative_ -* **Y23f6** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result unknown_ +- **Y20d1** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result positive_ +- **Y20d2** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result negative_ +- **Y23f6** _SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) RNA (ribonucleic acid) detection result unknown_ These are coded in response to data flowing from Pillar 1 and Pillar 2. (At the time of writing, Dec 2020, Moonshot community tests are also planned to be incorporated). @@ -44,22 +43,25 @@ However, invalid or unusual dates are possible and may occur for a number of rea Clinical codes relating to certain conditions or situations, as defined in the Royal College of GP’s (RCGP) sensitive datasets, are not available in OpenSAFELY. These are: -* **Gender related issues**: SNOMED Refset for General Practice summary data sharing exclusion for gender related issues _999004351000000109_ -* **Assisted fertility**: SNOMED Refset for General Practice summary data sharing exclusion for assisted fertility _999004371000000100_ -* **Termination of pregnancy**: SNOMED Refset for General Practice summary data sharing exclusion for termination of pregnancy _999004361000000107_ -* **Sexuality and sexual activity**: Finding related to sexuality and sexual activity _All children of the SNOMED code 118199002_ +- **Gender related issues**: SNOMED Refset for General Practice summary data sharing exclusion for gender related issues _999004351000000109_ +- **Assisted fertility**: SNOMED Refset for General Practice summary data sharing exclusion for assisted fertility _999004371000000100_ +- **Termination of pregnancy**: SNOMED Refset for General Practice summary data sharing exclusion for termination of pregnancy _999004361000000107_ +- **Sexuality and sexual activity**: Finding related to sexuality and sexual activity _All children of the SNOMED code 118199002_ ## Additional derived data ### Geographic and administrative groupings + A patient registers with a practice using their home address. The postcode from this address is mapped to an Output Area, from which other larger geographic representations such as LSOA, MSOA, CCG, and STP can be derived (see [various](https://geoportal.statistics.gov.uk/search?q=Beginners%20Guide%20to%20UK%20Geographies) [ONS publications](https://www.ons.gov.uk/methodology/geography/ukgeographies) for more detail). #### MSOA + According to our identifiable data minimisation principles, only representations as large or larger than MSOA are available to be extracted into a study cohort for analysis. Of ~36 million active patient addresses, less than 55,000 have no MSOA code set. These are a split of no postcode entered, an invalid postcode entered, and no fixed abode. #### IMD + IMD ([Index of Multiple Deprivation](https://www.gov.uk/government/statistics/english-indices-of-deprivation-2019)) is a ranking of LSOAs based on various characteristics of the areas. The original ranking ranges from 1 to 32,844 (the number of LSOAs in England), where 1 is the most deprived area. @@ -80,9 +82,9 @@ In these cases, the rounded ranking is -1. Occasionally, a patient has multiple active registrations on a given date. If so, the address is chosen as follows: -* choose the registration with the latest start date; -* if this is not unique, then choose the registration with the latest end date; -* if this is not unique, then choose the registration with the lowest ID. +- choose the registration with the latest start date; +- if this is not unique, then choose the registration with the latest end date; +- if this is not unique, then choose the registration with the lowest ID. If a patient's address is not recorded, then these geographic variables are not available for analysis. @@ -90,17 +92,16 @@ If a patient's address is not recorded, then these geographic variables are not Content to be written. - ## Externally linked data Patient records from external datasets are imported and matched to the core primary care data as follows: -* Patient records from other external sources are matched to SystmOne records on NHS numbers via a [salted](https://en.wikipedia.org/wiki/Salt_(cryptography)) [hash](https://en.wikipedia.org/wiki/Cryptographic_hash_function): - * Usually this is done by the data controllers of the external dataset — that is, hashed NHS numbers for patients in OpenSAFELY are sent to the external data controller, they identify all the matching records in their dataset, and then send only those records back to OpenSAFELY. - * For some datasets (ICNARC), OpenSAFELY receives the hashed NHS numbers from the external dataset and the matching occurs inside OpenSAFELY. The matched IDs are then sent back and the matched records are returned to OpenSAFELY. -* No other identifiers (names, postcodes, DOBs etc) are used for matching, though this may change in future. -* No patient identifiers are imported from external datasets. -* Only records for patients with matching NHS numbers are imported to OpenSAFELY (i.e., `left_join(SystmOne, External, by='NHSNumber')`). +- Patient records from other external sources are matched to SystmOne records on NHS numbers via a [salted]() [hash](https://en.wikipedia.org/wiki/Cryptographic_hash_function): + - Usually this is done by the data controllers of the external dataset — that is, hashed NHS numbers for patients in OpenSAFELY are sent to the external data controller, they identify all the matching records in their dataset, and then send only those records back to OpenSAFELY. + - For some datasets (ICNARC), OpenSAFELY receives the hashed NHS numbers from the external dataset and the matching occurs inside OpenSAFELY. The matched IDs are then sent back and the matched records are returned to OpenSAFELY. +- No other identifiers (names, postcodes, DOBs etc) are used for matching, though this may change in future. +- No patient identifiers are imported from external datasets. +- Only records for patients with matching NHS numbers are imported to OpenSAFELY (i.e., `left_join(SystmOne, External, by='NHSNumber')`). Matching quality is dependent on the quality of NHS numbers (they're good but not infallible). Currently there is no direct evaluation of linkage quality because by design (minimisation of the transfer of sensitive data) we don't have access to direct identifiers from external datasets; nor do we know in general if we should be expecting a match or not. @@ -108,6 +109,7 @@ Currently there is no direct evaluation of linkage quality because by design (mi When TPP receive data from external data sources (eg ONS), the tables are completely replaced. ## OpenSAFELY-TPP database builds + The OpenSAFELY-TPP database is typically built once per week. In essence, this involves refreshing the database records so that the following groups are available for analysis: @@ -123,9 +125,6 @@ Old database builds cannot be recovered, and due to the differences between succ For those with access to the OpenSAFELY database, the latest database build time is available in the `LatestBuildTime` table, and the history of builds for each dataset is available in the `BuildInfo` table. - - - ## OpenSAFELY-TPP database coverage and metadata - [Most recent coverage of records in SystmOne and external datasets](https://reports.opensafely.org/reports/opensafely-tpp-database-builds/) @@ -133,6 +132,4 @@ For those with access to the OpenSAFELY database, the latest database build time - [OpenSAFELY-TPP database schema](https://reports.opensafely.org/reports/opensafely-tpp-database-schema/) - [OpenSAFELY-TPP database table examples (based on dummy data)](https://github.com/opensafely/tpp-sql-notebook/blob/master/notebooks/tpp-schema.ipynb) - -[^1]: - "Registered" here means a patient with a full "GMS" (General Medical Services) registration. Patients with temporary registrations are not included. +[^1]: "Registered" here means a patient with a full "GMS" (General Medical Services) registration. Patients with temporary registrations are not included. diff --git a/docs/data-sources/therapeutics.md b/docs/data-sources/therapeutics.md index c16e4e6b4..82746f849 100644 --- a/docs/data-sources/therapeutics.md +++ b/docs/data-sources/therapeutics.md @@ -2,31 +2,54 @@ The Therapeutics dataset contains information on COVID treatments used in inpati ## Metadata -* **Data provider** NHS England -* **Participation / Coverage** Inpatients and outpatients treated with antivirals/nMABs for COVID-19 in England -* **Provenance** Data sourced largely from BlueTeq system (forms completed by clinicians) -* **Update frequency in OpenSAFELY** Approximately weekly -* **Delay between event occurring and event appearing in OpenSAFELY** Approximately 2-9 days -* **Collected information** Treatment start date; therapeutic intervention; COVID indication, current status, risk group, region +**Data provider** +: NHS England +**Participation / Coverage** +: Inpatients and outpatients treated with antivirals/nMABs for COVID-19 in England + +**Provenance** +: Data sourced largely from BlueTeq system (forms completed by clinicians) + +**Update frequency in OpenSAFELY** +: Approximately weekly + +**Delay between event occurring and event appearing in OpenSAFELY** +: Approximately 2-9 days + +**Collected information** +: Treatment start date; therapeutic intervention; COVID indication, current status, risk group, region ## Overview + Antivirals and neutralising monoclonal antibodies (nMABs) for COVID-19 can be administered in inpatient setting or, for outpatients, in COVID Medicine Delivery Units (CMDUs) specifically set up for this purpose. For patients considered for these treatments, clinicians submit completed forms to NHS England. Each row represents one completed form for one course of treatment. Data received by OpenSAFELY currently covers patients who were approved for treatment. The patient may or may not have actually received the treatment or completed the course (but we assume that they usually do). They may have another form completed for another treatment, either because it was decided to give them a different treatment, or for some other reason. They may in theory also have another form completed some months later for another instance of infection. Treatment dates may be in the past or future at the point when the form is submitted. - ## More Information -* [Treatment guidelines](https://www.nice.org.uk/guidance/ta878) +- [Treatment guidelines](https://www.nice.org.uk/guidance/ta878) ## Datasource-specific glossary -* **date**: From `TreatmentStartDate`. This is entered by the clinician completing the form and may be in the past, future or the same date on which the form is submitted. -* **therapeutic**: Name of treatment(s) given. When used as a `returning` option, is a comma-separated string from `Intervention` (removing " and "). -* **region**: The region is one of seven NHS regions, derived from the NHS Trust/site from which the form was submitted. -* **risk group**: This is present for outpatients only. Derived from tick boxes on the form for Molnupiravir, Sotrovimab and Casivirimab combined into one comma-separated string. May return duplicates to be resolved e.g. "cancer,cancer". Can be missing (if clinician selected "Other" and supplied risk group as free text). Risk groups are only returned if they match [a defined set of available values](https://github.com/opensafely-core/cohort-extractor/blob/main/cohortextractor/therapeutics_utils.py#L23). -* **with_these_therapeutics**: As `therapeutic` above. Filters on `Intervention`. Case insensitive. Currently available options: 'remdesivir', 'tocilizumab', 'sarilumab', 'casirivimab and imdevimab', 'molnupiravir', 'sotrovimab', 'paxlovid'. -* **with_these_statuses**: Filters on `CurrentStatus`. Should be one or more of 'Approved', 'Treatment Complete', 'Treatment Not Started', 'Treatment Stopped'. +**date** +: From `TreatmentStartDate`. This is entered by the clinician completing the form and may be in the past, future or the same date on which the form is submitted. + +**therapeutic** +: Name of treatment(s) given. When used as a `returning` option, is a comma-separated string from `Intervention` (removing " and "). + +**region** +: The region is one of seven NHS regions, derived from the NHS Trust/site from which the form was submitted. + +**risk group** +: This is present for outpatients only. Derived from tick boxes on the form for Molnupiravir, Sotrovimab and Casivirimab combined into one comma-separated string. May return duplicates to be resolved e.g. "cancer,cancer". Can be missing (if clinician selected "Other" and supplied risk group as free text). Risk groups are only returned if they match [a defined set of available values](https://github.com/opensafely-core/cohort-extractor/blob/main/cohortextractor/therapeutics_utils.py#L23). + +**with_these_therapeutics** +: As `therapeutic` above. Filters on `Intervention`. Case insensitive. Currently available options: 'remdesivir', 'tocilizumab', 'sarilumab', 'casirivimab and imdevimab', 'molnupiravir', 'sotrovimab', 'paxlovid'. + +**with_these_statuses** +: Filters on `CurrentStatus`. Should be one or more of 'Approved', 'Treatment Complete', 'Treatment Not Started', 'Treatment Stopped'. Case insensitive. -* **with_these_indications**: Filters on COVID_indication. Should be one or more of 'non-hospitalised', 'hospital_onset', 'hospitalised_with'. + +**with_these_indications** +: Filters on COVID_indication. Should be one or more of 'non-hospitalised', 'hospital_onset', 'hospitalised_with'. diff --git a/docs/data-sources/ukrr.md b/docs/data-sources/ukrr.md index 07f2536b2..535c8394d 100644 --- a/docs/data-sources/ukrr.md +++ b/docs/data-sources/ukrr.md @@ -2,13 +2,21 @@ The UK Renal Registry (UKRR) contains data on patients under secondary renal car care delivery in the UK especially dialysis and kidney transplant. Data is collected from many different renal IT systems. !!! warning - UKRR data can only be used subject to additional approvals. - Please contact your co-pilot, or if you have any questions. + UKRR data can only be used subject to additional approvals. Please contact your co-pilot, or if you have any questions. There are 5 different datasets available to OpenSAFELY. These are: -* **2019_prevalence** *a prevalence cohort of patients alive and on RRT in December 2019* -* **2020_prevalence** *a prevalence cohort of patients alive and on RRT in December 2020* -* **2021_prevalence** *a prevalence cohort of patients alive and on RRT in December 2021* -* **2020_incidence** *an incidence cohort of patients who started RRT in 2020* -* **2020_ckd** *a snapshot prevalence cohort of patient with Stage 4 or 5 CKD who were reported to the UKRR to be under renal care in December 2020* +**2019_prevalence** +: a prevalence cohort of patients alive and on RRT in December 2019 + +**2020_prevalence** +: a prevalence cohort of patients alive and on RRT in December 2020 + +**2021_prevalence** +: a prevalence cohort of patients alive and on RRT in December 2021 + +**2020_incidence** +: an incidence cohort of patients who started RRT in 2020 + +**2020_ckd** +: a snapshot prevalence cohort of patient with Stage 4 or 5 CKD who were reported to the UKRR to be under renal care in December 2020 diff --git a/mkdocs.yml b/mkdocs.yml index 2b3f6993e..0d35e6c3e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -180,6 +180,7 @@ watch: - includes markdown_extensions: + - def_list - pymdownx.details - pymdownx.snippets: check_paths: true From ea1d4f07757f10111cd85213286ae622b7af8026 Mon Sep 17 00:00:00 2001 From: Thomas O'Dwyer Date: Wed, 28 Jan 2026 13:32:39 +0000 Subject: [PATCH 3/3] Update data sources index page --- docs/data-sources/index.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/data-sources/index.md b/docs/data-sources/index.md index fb3c2b45f..bb42cff16 100644 --- a/docs/data-sources/index.md +++ b/docs/data-sources/index.md @@ -2,20 +2,24 @@ - [Overview](./intro.md) -## Datasets available for all research under the New Direction +## Datasets available for all research -- [SystmOne primary care (General Practice coded events)](./systmone.md) +- [Emergency attendances](./ecds.md) +- [EMIS primary care](./emis.md) - [Hospital admissions (hospital spells, outpatients and A&E)](./apc.md) - [ONS Registered Deaths](./onsdeaths.md) +- [SystmOne primary care (General Practice coded events)](./systmone.md) -## Other datasets under the COVID Direction +## Datasets available for COVID-19 research -- [EMIS primary care](./emis.md) +- [Airmid (PROMPT)](../ehrql/reference/schemas/tpp.md#open_prompt) - [Covid-19 test results](./sgsscovid.md) - [Covid-19 therapeutics](./therapeutics.md) -- [Emergency attendances](./ecds.md) +- [HealthCareWorker](/ehrql/reference/schemas/tpp/#occupation_on_covid_vaccine_record) - [High Cost Drugs](./hcd.md) - [In-hospital deaths (covid-19 only)](./cpns.md) - [Intensive care admissions (covid-19 only)](./icnarc.md) - [International Severe Acute Respiratory and emerging Infection Consortium](./isaric.md) - [UK Renal Registry](./ukrr.md) +- [Waiting List clockstops](../ehrql/reference/schemas/raw.tpp.md#wl_clockstops) +- [Waiting List openpathways](../ehrql/reference/schemas/raw.tpp.md#wl_openpathways)