Post #1700478

2026-04-24 18:46 UTC

Would anyone have advice on FOSS tooling for reproducible biomedical literature searches? What I&#39;d want to do specifically is to document the *absence* of case reports of exceptional responses to drugs that got FDA accelerated approval. (As for why, see https://osf.io/59sya/files/q6trp.) These would start with automated searches of EuropePMC, then annotation of manual review results. Since a new case report could be published at any time, I would need these to be update-able. I&#39;m guessing an approach built on #orgmode #make and other #root technologies could work well. @lukascbossert @jameshowell #reproducibleresearch

Replies (3)

@jameshowell@fediscience.org 2026-04-24 19:01

@dcnorris@scicomm.xyz My own guess is that automating searches and even partly automating their annotation is the easy part. The hard part is likely to be demonstrating that absence of search results means absence of search targets. @lukascbossert@mastodon.social

Open ##2252558
@lukascbossert@mastodon.social 2026-04-25 07:28

@dcnorris@scicomm.xyz @jameshowell@fediscience.org Interesting question. I guess it depends also much whether the databases offer an API that you can use with a #root tool - however i guess #curl is very much capable of this. once the script is written I‘d use a CI/CD pipeline for getting regular (non)results.

Open ##2252560
@lymphomation@mastodon.social 2026-04-25 12:07

@dcnorris@scicomm.xyz @lukascbossert@mastodon.social @jameshowell@fediscience.org On recall, Dave, the Exceptional Responder study was designed to identify drug targets that may be applicable to certain individuals (via biomarkers); that it was exploratory. I do not think it led to any FDA approvals but I could be wrong of course. Findings may have justified some expanded access applications by patients and their doctors.

Open ##2252562