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EBISPOT / xgwas-curator-tasks

An internal repo for GWAS curators to track issues
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Pass on any gene burden papers to Open targets #13

Closed ljwh2 closed 1 year ago

ljwh2 commented 1 year ago

Open targets are ingesting gene burden analyses, but they don't have any systematic way to identify these. A curator should review the lit search list and identify all the studies from the last 6m-1yr, to pass on to Open Targets. This could be done monthly going forward.

ljwh2 commented 1 year ago

@earlEBI I realised we said longer than 1 yr in the meeting just now, maybe start with 6m-1 year and see how time consuming it is

earlEBI commented 1 year ago

@ljwh2 I've added a gene-based tab to the literature triage Google Sheets doc. There's a list of 37 gene-based GWAS publications, searching from April 2022 onwards. I cleaned up the 'gwas catalog outcome' column to hopefully make sense to Open Targets. Only checked [and removed quite a few of] those with ambiguous triage comments. Otherwise, inclusion is based on triage comment only.

earlEBI commented 1 year ago

Just curating a publication which I notice also carried out gene-based analysis (PMID 36699085). I don't think most papers which carry out both SV and gene-based will be noted in the literature triage? Should curators just add them to the sheet as we come across them?

ljwh2 commented 1 year ago

You're right, they won't and that's a good idea to ask curators to note them in the tab in the literature triage sheet