Disclaimer: Before retiral I was a Biomedical Scientist for NHS Scotland. My area of specialty was Microbiology, but since 1998ish I looked after IT matters for the Microbiology Lab. Initially this meant overseeing the implementation of a resource management package, but soon spread into making sure the 3 PCs we had for general use in the "computer room" (a large cupboard, shared with a freeze drier...) ticked over, and supporting those hardy souls who were dipping their toe into the word processing water. Like a lot of folk in this situation, it soon became "if it had a plug on it, it was mine".
When we rolled out the Lab IT System I became responsible for retrieving data for all sorts of purposes, for all sorts of people as well as managing the 50-odd PCs in the lab and making sure that our analysers could talk to the lab system.
My role in this was fairly unique in that right up until I retired in 2019, few diagnostic labs in the UK using Lab systems from our supplier had dedicated IT people. Mostly, the data mining was done by staff in between doing actual lab or management duties.
My experience of data mining in Diagnostic Labs was that it was either done using direct queries on the database (Uniquery latterly, but an earlier supplier used SQL) or since 2016, writing Business Objects queries against a Universe supplied by the Lab System people. The rather crappy data structures produced by these queries were usually imported into excel for further processing, with all the headaches that entails (leading zeros being stripped off our 10 digit patient identifier being a favourite

).
This worked ok with the reasonably small numbers produced by "How many Organism x sensitive to antibiotic y in ward z did we get last year?" style queries, but the occasional one that produced thousands of lines was a nightmare. Then you pass the data to people who only have a vague idea of what they wanted in the first place, and an even vaguer idea of what to do with it when they got it.
So I can see why lots of small Labs, running a variety of competing Lab Systems, might not be able to supply the data in a format that the collators wanted. And if I remember correctly, Business Objects didn't export XLSX files...