Hi BugSigDB team,

Just a heads up that I’ve integrated bugsigdbr into the TaxSEA package, which performs taxon set enrichment analysis for microbiome data. Past versions of TaxSEA were built around a static database but we're beginning to build out some more ways to keep this updated.

The latest version of TaxSEA(v1.1.2 on bioconductor devel branch) dynamically fetches BugSigDB using bugsigdbr::importBugSigDB() and getSignatures(..., tax.id.type = "ncbi"), rather than relying on a static internal database. I’ve designed it to fail gracefully if bugsigdbr is not installed (TaxSEA leverages multiple databases and allows for custom set analyses too). Currently it's just returning the full name from BugSigDB (e.g. bsdb_bsdb:34622226/1/2_Colorectal-cancer) and we point users towards the bugsigdbr package for further annotation. However in the future I'll hopefully pull some of this information directly into that TaxSEA output (E.g. Year of publication, journal, study title) to make things a bit more legible for users and easier plotting.

I wanted to flag this in case future changes to the API (e.g. renaming columns, altering return formats, or changing ID fields) are being considered. Happy to adjust on my end if anything does change but wanted to share this in the spirit of collaboration.

PS if there is a way to keep updated on BugSigDB developments (mailing list? slack? or something else?) let me know.

Thanks again for maintaining this great resource!
Feargal