opensafely-core / opensafely-core/opencodelists

Have metadata that describes when a codelist has been used in a paper

Open
#42 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

duplicate enhancement
Dominant language
Python
Stars
60
Forks
16
Avg merge
4d 12h
Merged PRs (30d)
17

Description

I got an email with a query:

We are producing a risk assessment for staff related to covid-19 infection based on best available evidence and OpenSAFELY as a major source. https://www.medrxiv.org/content/10.1101/2020.05.06.20092999v1.full.pdf Our colleagues noticed an inconsistency in ethnicity classification, in particular, what is meant by Asian British. I think it is a redundant description because British nationality is not used in other ethnic groups but would like to check with the authors first. With many thanks for your kind reply,

Through the magic of opencodelists I was able to reply

Thanks. It is Asian, rather than Asian British, yes. You can view the full codelists used here https://codelists.opensafely.org/?q=ethnicity

And they were pleased

Thank you so much for your reply and sharing the codes so we also understand the subgroups. Very much appreciated for your help.

So, another feelgood example of the benefits of sharing codelists and code.

But one thing: it wasn't immediately clear from opencodelists which of the two ethnicity lists currently present was used in this paper. (I think it's the CTV3 one, and the SNOMED one is made by mapping magic by Peter? Or imported as an interim from elsewhere?). Anyway, I know usage metadata is on the roadmap, just wanted to briefly log this as a situation where it would have been useful to have a field that says:

Usage "This codelist was used in the following analyses / repos / papers: X Y Z"

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing how OpenCodelists currently identifies and presents the two ethnicity codelists mentioned in the issue. Define what usage metadata should cover across analyses, repositories, and papers, then confirm that a codelist's page clearly shows the relevant usage references.

Written by the indexing model from the issue text.

Assessment

Domain
content
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.