Add a column to the studies download to indicate CNV studies

[eks-ebi]

Background

• CNV (copy number variation) studies are GWAS that look at a different kind of genetic variant compared to the SNPs identified in standard GWAS.
• At an earlier stage of the GWAS Catalog, some (~57) CNV studies were curated, but it was later decided that these were outside the Catalog's scope. No new CNV studies were curated after 2012.
• The existing CNV studies were removed from the public Catalog (UI, downloads etc.). They still exist in the database and have Curation Status = "CNV Paper" and Curator = "Unassigned".
• There is a CNV column in the All associations downloads, with possible values "Y" or "N" to show whether the association came from a CNV study or not. All associations currently visible in the download have "N" in this column.
• There is no CNV column in the All studies downloads.

Current issue

• We recently made the decision to allow summary statistics submissions for CNV studies, however we will not curate any associations for these studies. So far we have received 1 CNV sumstats submission: 6138bb606d0dd70001adccca (and one pending, May 2022)

User stories

• As a curator, I need to be able to indicate that the new CNV+sumstats studies are CNV studies, to show users that they are different from the typical studies in the Catalog. The logical place for this is the study-level checkboxes.
• As a user, I want to be able to identify CNV studies that are linked to summary stats, and access the relevant metadata. There should be a column in the All studies download to indicate studies that are CNV studies. This information should also be visible in the UI. I do not want to see any information associated with the older CNV studies with no summary statistics.

To do

In first iteration, we need to fulfil the curator user story and implement the changes to the download. Ui changes could be later. There is other information we don't display in the UI, such as GxE, GXG. There could be an additional field on the study page something like: "Study type" where this information could be displayed, e.g. Study type: CNV analysis or Study type: interaction study. We would need to think of a default term to cover all the standard GWAS.

[eks-ebi]

@ljwh2 please add comments/corrections as needed

[ljwh2]

Updated with comments as we now have a second CNV submission in the pipeline, and the first is published

[ljwh2]

Notes, current CNV submissions are GCP000324 and PMID35240056