Covers: the Hub-based route for experiment data and annotation packages (chapters 14 “Package data” and the “Non-software packages” chapter), and the HubPub CreateAHubPackage vignette.
Hub-based data packages (ExperimentHub / AnnotationHub)
Large data belongs in a Hub, not in the package tarball. A Hub package ships code and metadata; the files live on Bioconductor’s storage and are fetched on demand.
What the package must contain
inst/extdata/metadata.csv: one row per resource with the fields the Hub requires (Title, Description, BiocVersion, Genome, SourceType, SourceUrl, SourceVersion, Species, TaxonomyId, Coordinate_1_based, DataProvider, Maintainer, RDataClass, DispatchClass, Location_Prefix, RDataPath, Tags).AnnotationHubData::makeAnnotationHubMetadata()(or the ExperimentHub equivalent) validates it; run it before submitting.inst/scripts/make-data.R: how every resource was produced from its source, so the data can be regenerated; andinst/scripts/make-metadata.R: howmetadata.csvwas written.- Accessor functions (or the generic Hub
query()shown in the vignette) documented inman/, with the provenance, source and license of each resource stated where a user will read it. - A vignette that retrieves at least one resource and shows what it is for. If a chunk cannot run at build time, say why in the text; do not leave the core retrieval as
eval=FALSEwithout a reason.
Before review
- Contact hubs@bioconductor.org and upload the data; the resources must be resolvable through the Hub before the package is reviewed, otherwise the vignette and examples cannot run and the reviewer cannot check the metadata against the data.
- Licenses and terms of use of the underlying data are stated per resource when they differ from the package license.
- Experiment data packages are submitted through the same GitHub tracker as software packages; annotation packages are sent by email to packages@bioconductor.org instead (see ../01-submissions.md).
BiocTypeisExperimentDataorAnnotation, andbiocViewscome from the matching single category (ExperimentDataorAnnotationData).
Source: Package data, Non-software packages (the “Hub packages” section), and the HubPub vignette CreateAHubPackage. Derived 2026-09-23 from data.md and non-software-pkgs.md (chapters fetched 2026-08-14, pkgrevdocs pin in ../SOURCES.md) and the HubPub vignette; refresh it with them.