diff --git a/docs/actions-pipelines.md b/docs/actions-pipelines.md index 12152122e..7e4869354 100644 --- a/docs/actions-pipelines.md +++ b/docs/actions-pipelines.md @@ -185,5 +185,3 @@ No data should ever be published from the Level 3 server. Access is only for per Highly sensitive outputs can be seen in `E:/high_privacy/workspaces/`. This includes a directory called `metadata`, containing log files for each action e.g. `generate_dataset.log`, `run_model.log`. Moderately sensitive outputs can be seen in `E:/FILESFORL4/workspaces/`. - ----8<-- 'includes/glossary.md' diff --git a/docs/actions-reusable.md b/docs/actions-reusable.md index 30f36537c..f4a1e11a2 100644 --- a/docs/actions-reusable.md +++ b/docs/actions-reusable.md @@ -87,5 +87,3 @@ When developing a reusable action, just as when developing a scripted action, th Its dependencies are in [*packages.csv*](https://github.com/opensafely-core/r-docker/blob/master/packages.csv). * The Stata runtime is provided by [`stata-docker`](https://github.com/opensafely-core/stata-docker). Its dependencies are in [*libraries*](https://github.com/opensafely-core/stata-docker/tree/main/libraries). - ----8<-- 'includes/glossary.md' diff --git a/docs/codelist-creation.md b/docs/codelist-creation.md index f2c160d17..604421832 100644 --- a/docs/codelist-creation.md +++ b/docs/codelist-creation.md @@ -149,7 +149,3 @@ on [our blog](https://www.bennett.ox.ac.uk/blog/2022/11/difference-between-bnf-d
- - - ----8<-- 'includes/glossary.md' diff --git a/docs/codelist-intro.md b/docs/codelist-intro.md index 9b8dcf9fa..c2a6cb6f4 100644 --- a/docs/codelist-intro.md +++ b/docs/codelist-intro.md @@ -44,7 +44,3 @@ any key decisions discussion and conversations will be available for examination - These discussions should be linked to from the website - i.e. link the issue to the final codelist where it appears in OpenSAFELY Codelists - - - ----8<-- 'includes/glossary.md' diff --git a/docs/codelist-project.md b/docs/codelist-project.md index 4042e9b68..7cd4579b1 100644 --- a/docs/codelist-project.md +++ b/docs/codelist-project.md @@ -52,5 +52,3 @@ This command should be re-run every time a codelist is added or removed from the If necessary, you can also import CSVs not via OpenCodelists - just manually copy the CSV files into `codelists/`. However, we would recommend uploading these to OpenCodelists to import them as above. Note, if you are _also_ using some codelists from OpenCodelists, any manually imported codelists should be stored in a `local_codelists` folder so that they are not overwritten in the next step, as manual changes to CSV files will be clobbered the next time the command is run. See more on using Codelists in your study definition in [Working with codelists](legacy/study-def-codelists.md). - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/apc.md b/docs/data-sources/apc.md index 0af9bb5a4..36b7e0dfa 100644 --- a/docs/data-sources/apc.md +++ b/docs/data-sources/apc.md @@ -89,6 +89,3 @@ Code | Description * [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) - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/cpns.md b/docs/data-sources/cpns.md index cce3f4deb..bac1922d3 100644 --- a/docs/data-sources/cpns.md +++ b/docs/data-sources/cpns.md @@ -15,7 +15,3 @@ Initially this was lab-confirmed covid deaths only, but also includes suspected * [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) - - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/ecds.md b/docs/data-sources/ecds.md index 0d71b6e05..94f45a3f9 100644 --- a/docs/data-sources/ecds.md +++ b/docs/data-sources/ecds.md @@ -20,8 +20,3 @@ Diagnoses and discharge destinations are coded using SNOMED CT. * [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 ) - - - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/icnarc.md b/docs/data-sources/icnarc.md index c6aaa4446..c86cdd9e7 100644 --- a/docs/data-sources/icnarc.md +++ b/docs/data-sources/icnarc.md @@ -36,6 +36,3 @@ Specialist units (eg neuro / cardiac) also participate. covid-19 admissions only 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. - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/intro.md b/docs/data-sources/intro.md index c2734ca2f..10fa7c1dc 100644 --- a/docs/data-sources/intro.md +++ b/docs/data-sources/intro.md @@ -12,5 +12,3 @@ GP records, or primary care records, can also be used for conducting health rese
- ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/isaric.md b/docs/data-sources/isaric.md index 965158966..1e1d580a4 100644 --- a/docs/data-sources/isaric.md +++ b/docs/data-sources/isaric.md @@ -4,6 +4,3 @@ The ISARIC dataset contains data from the International Severe Acute Respiratory !!! warning This section is a work in progress. - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/onsdeaths.md b/docs/data-sources/onsdeaths.md index 9bd92712f..55cfbc972 100644 --- a/docs/data-sources/onsdeaths.md +++ b/docs/data-sources/onsdeaths.md @@ -21,6 +21,3 @@ Causes of death are coded using ICD-10. ## 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. - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/systmone.md b/docs/data-sources/systmone.md index 02230ee4c..fab7d9923 100644 --- a/docs/data-sources/systmone.md +++ b/docs/data-sources/systmone.md @@ -124,5 +124,3 @@ For those with access to the OpenSAFELY database, the latest database build time [^1]: "Registered" here means a patient with a full "GMS" (General Medical Services) registration. Patients with temporary registrations are not included. - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/therapeutics.md b/docs/data-sources/therapeutics.md index f2bd6f06e..c16e4e6b4 100644 --- a/docs/data-sources/therapeutics.md +++ b/docs/data-sources/therapeutics.md @@ -30,6 +30,3 @@ Treatment dates may be in the past or future at the point when the form is submi * **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'. - - ----8<-- 'includes/glossary.md' diff --git a/docs/data-sources/ukrr.md b/docs/data-sources/ukrr.md index 8e38e3e17..07f2536b2 100644 --- a/docs/data-sources/ukrr.md +++ b/docs/data-sources/ukrr.md @@ -1,5 +1,5 @@ -The UK Renal Registry (UKRR) contains data on patients under secondary renal care (advanced chronic kidney disease stages 4 and 5, dialysis, and kidney transplantation). The purpose of the UKRR is to audit secondary kidney -care delivery in the UK especially dialysis and kidney transplant. Data is collected from many different renal IT systems. +The UK Renal Registry (UKRR) contains data on patients under secondary renal care (advanced chronic kidney disease stages 4 and 5, dialysis, and kidney transplantation). The purpose of the UKRR is to audit secondary kidney +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. @@ -12,5 +12,3 @@ There are 5 different datasets available to OpenSAFELY. These are: * **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* - ----8<-- 'includes/glossary.md' diff --git a/docs/five-safes.md b/docs/five-safes.md index e1bf1e468..5c65644b7 100644 --- a/docs/five-safes.md +++ b/docs/five-safes.md @@ -7,6 +7,3 @@ OpenSAFELY follows the [Five Safes](https://ukdataservice.ac.uk/help/secure-lab/ * **Safe outputs** - is there any residual risk in outputs being released from the environment? You can read more about how we use the Five Safes Framework to design the OpenSAFELY platform in our blog post [The ‘Five Safes’ Framework and applying it to OpenSAFELY](https://www.bennett.ox.ac.uk/blog/2023/03/the-five-safes-framework-and-applying-it-to-opensafely/). - - ----8<-- 'includes/glossary.md' diff --git a/docs/git-workflow.md b/docs/git-workflow.md index dc2ef1f1d..da668c457 100644 --- a/docs/git-workflow.md +++ b/docs/git-workflow.md @@ -38,5 +38,3 @@ For a more generic overview, see [GitHub's own guidance](https://guides.github.c ![Writing a commit message with GitHub Desktop.](images/getting-started-github-desktop-commit-message.png) 1. Click **Push origin** to push your local changes to the remote repository on GitHub ![Pushing changes to GitHub with GitHub Desktop.](images/getting-started-github-desktop-push-to-github.png) - ----8<-- 'includes/glossary.md' diff --git a/docs/how-to-get-help.md b/docs/how-to-get-help.md index c09d63030..a117150da 100644 --- a/docs/how-to-get-help.md +++ b/docs/how-to-get-help.md @@ -88,5 +88,3 @@ please use our [Q&A forum](https://github.com/opensafely/documentation/discussio To discuss making your data available to researchers via the OpenSAFELY platform, please [contact our technical team](mailto:team@opensafely.org). - ----8<-- 'includes/glossary.md' diff --git a/docs/index.md b/docs/index.md index 51ba60f4b..1db25d4d1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -73,5 +73,3 @@ See our guidance for [system integrators and data providers](system-integration. !!! note "These documents are a work-in-progress" Please see the [Updating the Documentation page](updating-the-docs.md) if you want to make improvements. - ----8<-- 'includes/glossary.md' diff --git a/docs/install-docker.md b/docs/install-docker.md index bfc85f4b9..38192bcc3 100644 --- a/docs/install-docker.md +++ b/docs/install-docker.md @@ -107,5 +107,3 @@ It is easy to think that it has frozen, but it will take quite a while to get go checking Control Panel > Administrative Tools > Services > Server was **Disabled**. Setting this to **Automatic** — the default in Windows — then started Docker running again. - ----8<-- 'includes/glossary.md' diff --git a/docs/install-python.md b/docs/install-python.md index e40b3adaa..b36f63c6b 100644 --- a/docs/install-python.md +++ b/docs/install-python.md @@ -87,6 +87,3 @@ Then enable this version (eg `3.10.1`) in pyenv: ```bash pyenv global system 3.10.1 ``` - - ----8<-- 'includes/glossary.md' diff --git a/docs/legacy/study-def-flowcharts.md b/docs/legacy/study-def-flowcharts.md index 35e8f40b4..b7fc53831 100644 --- a/docs/legacy/study-def-flowcharts.md +++ b/docs/legacy/study-def-flowcharts.md @@ -10,6 +10,3 @@ Many studies will require a flowchart to show inclusion/exclusion of patients in - Make a copy of the study definition (called `study_definition_flow_chart.py`). The `population=patients.satisfying()` function should be replaced with `population=patients.all()`. Then all variables except for those that appeared in the population definition logic should be removed (this will mean that it runs much faster than the main study definition). An example of such a study definition can be seen in [this repository on NSAIDS use and COVID-related outcomes](https://github.com/opensafely/nsaids-covid-research/commit/e5ad58c72926d7c73ba131099486409f6876883d). - Then write a script that reads the `input_flow_chart.csv` and then sequentially drops each of the variables and counts the remaining population, in whatever order you'd like to report them; [Stata example](https://github.com/opensafely/nsaids-covid-research/blob/23069312944ea1fc6d79ec4d9b45eea25df96ab0/analysis/flowchart_numbers.do). - - ----8<-- 'includes/glossary.md' diff --git a/docs/legacy/study-def-measures.md b/docs/legacy/study-def-measures.md index fc0b8d84c..28b1e92e5 100644 --- a/docs/legacy/study-def-measures.md +++ b/docs/legacy/study-def-measures.md @@ -221,5 +221,3 @@ To generate the final outputs `measure_hosp_admission_by_stp.csv.gz` and `measur measure_csv: output/measures/measure_*.csv.gz ``` - ----8<-- 'includes/glossary.md' diff --git a/docs/legacy/study-def-variables.md b/docs/legacy/study-def-variables.md index bc7694afb..a40b476d2 100644 --- a/docs/legacy/study-def-variables.md +++ b/docs/legacy/study-def-variables.md @@ -235,6 +235,3 @@ These variables create new variable from existing variables. They do not extract ::: cohortextractor.patients.which_exist_in_file   - - ----8<-- 'includes/glossary.md' diff --git a/docs/legacy/study-def.md b/docs/legacy/study-def.md index 34d83f368..167bc911b 100644 --- a/docs/legacy/study-def.md +++ b/docs/legacy/study-def.md @@ -343,5 +343,3 @@ actions: cohort: output/input-2020-09-01.csv.gz ``` Currently the study definition called above must have the index date defined within the StudyDefinition (e.g. `index_date="2020-01-01"`), though the date defined is arbitrary and is replaced by the arguments defined above. - ----8<-- 'includes/glossary.md' diff --git a/docs/open-data-manifesto.md b/docs/open-data-manifesto.md index b5bb9a172..011279b5c 100644 --- a/docs/open-data-manifesto.md +++ b/docs/open-data-manifesto.md @@ -28,6 +28,3 @@ Operational research is key to understanding what works in the NHS. However the * Use **version control**. * Write **tests** for your code. * Help develop and follow local **conventions** around coding. - - ----8<-- 'includes/glossary.md' diff --git a/docs/open-methods.md b/docs/open-methods.md index 9cfc8236e..6cb93a397 100644 --- a/docs/open-methods.md +++ b/docs/open-methods.md @@ -1,14 +1,10 @@ -We are using modern open working methods to carry out important analyses whilst preserving patient privacy and keeping all patient data secure. +We are using modern open working methods to carry out important analyses whilst preserving patient privacy and keeping all patient data secure. ## What do we mean by Open Working Methods? -We believe that researchers should be openly sharing all analytic cods and development insights in order to accelerate development of analyses and tools by other groups with other datasets. +We believe that researchers should be openly sharing all analytic cods and development insights in order to accelerate development of analyses and tools by other groups with other datasets. -Our tools are build using Python, SQL and Docker. Analyses can be carried out in Python, R or Stata. -All our code including analytic code is shared on GitHub and is open access for efficiency, reuse and collaboration. -We encourage external review and reuse of our code. - - - ----8<-- 'includes/glossary.md' +Our tools are build using Python, SQL and Docker. Analyses can be carried out in Python, R or Stata. +All our code including analytic code is shared on GitHub and is open access for efficiency, reuse and collaboration. +We encourage external review and reuse of our code. diff --git a/docs/output-checking.md b/docs/output-checking.md index 2dd84c96a..d4754b2f1 100644 --- a/docs/output-checking.md +++ b/docs/output-checking.md @@ -22,6 +22,3 @@ Below are the most common problems encountered by output checkers when reviewing 5. **Unsupported file types being requested**. Files requested for release should be one of the [allowed file types](requesting-file-release.md#allowed-file-types). If you are requesting the release of HTML files, please make sure you have followed the [guidance for HTML files](requesting-file-release.md#allowed-file-types). **~10%** of rejected outputs are due to unsupported file types being requested. To help avoid these issues, please make sure you have read the [checklist](requesting-file-release.md#checklist) before submitting your review request. - - ----8<-- 'includes/glossary.md' diff --git a/docs/protocol.md b/docs/protocol.md index 87671c716..0f9355e56 100644 --- a/docs/protocol.md +++ b/docs/protocol.md @@ -8,5 +8,3 @@ Briefly, pre-specifying your research question and developing a study protocol w Taken together, this can improve both the quality and credibility of your research. Developing a detailed study plan, including figure and table shells, can be particularly helpful when using a federated analytics platform such as OpenSAFELY, as there is less scope for interactively developing these whilst working with the data. This page will eventually contain resources for how to develop an effective study protocol, as well as tips for how to pre-register these formally on [OSF](https://osf.io/) or [ENCePP](http://www.encepp.eu/), or informally by uploading "locked" protocol versions to GitHub. There is no specific template for a protocol that you should use when working with OpenSAFELY, but you can see examples of protocols we've written for OpenSAFELY studies on most of our public repositories — for example [this inhaled corticosteroid (ICS) research repository](https://github.com/opensafely/ics-research/tree/master/protocol) or [this ethnicity research repository](https://github.com/opensafely/ethnicity-covid-research/tree/master/protocol). - ----8<-- 'includes/glossary.md' diff --git a/docs/releasing-files-intro.md b/docs/releasing-files-intro.md index a74d2d741..d8e1f30f9 100644 --- a/docs/releasing-files-intro.md +++ b/docs/releasing-files-intro.md @@ -8,6 +8,3 @@ In OpenSAFELY, there are 4 key “Safe Outputs” activities: 2. [Requesting release of outputs from the Level 4 server](requesting-file-release.md) that are necessary to fulfil the purpose of a project. 3. [Review of the requested outputs](output-checking.md) by two trained OpenSAFELY output checkers. 4. [Release of outputs that meet our disclosure rules](releasing-files.md) to the relevant workspace on the [Jobs site](jobs-site.md). - - ----8<-- 'includes/glossary.md' diff --git a/docs/releasing-files.md b/docs/releasing-files.md index 0044c6714..4d49fbdce 100644 --- a/docs/releasing-files.md +++ b/docs/releasing-files.md @@ -17,6 +17,3 @@ If you have had [intermediate data released](requesting-file-release.md#release- ### Reporting a data breach If you discover files released to the Jobs site that have been insufficiently redacted and still contain sensitive information, you should immediately contact and email the following (providing as much information as possible): Amir Mehrkar (); Ben Goldacre (); [disclosurecontrol@opensafely.org](mailto:disclosurecontrol@opensafely.org); and your co-pilot. Ensure you do not share these files and if they have already been shared please identify as best as possible with whom they have been shared. - - ----8<-- 'includes/glossary.md' diff --git a/docs/repositories.md b/docs/repositories.md index 01008ba0e..fe3c0aac6 100644 --- a/docs/repositories.md +++ b/docs/repositories.md @@ -129,7 +129,3 @@ If you want to create an empty folder to save files in, but you _never_ want its ``` This can be useful if you want to, for example, add a `output/plots/` subfolder to put your analysis plots into without having to check and create that folder explicitly every time in the analysis script. This is necessary because the contents of the `output/` folder is ignored by the default `.gitignore` in the root (the top-level) of the repository. - - - ----8<-- 'includes/glossary.md' diff --git a/docs/requesting-file-release.md b/docs/requesting-file-release.md index 2c768d971..00ced35ca 100644 --- a/docs/requesting-file-release.md +++ b/docs/requesting-file-release.md @@ -110,6 +110,3 @@ Once you have completed this form, please send it to **