All tables rebuilt from Ensembl 116 (previously Ensembl 114). Recipes are
pinned to the June 2026 archive, jun2026.archive.ensembl.org.
Recipes select data by species, and BioMart always returns whatever assembly is current for that species, so several datasets moved to a new assembly with this release:
| Dataset | Species | Assembly now served |
|---|---|---|
| grch38 | Human | GRCh38 |
| grch37 | Human | GRCh37 |
| grcm39 | Mouse | GRCm39 |
| grcr8 | Rat | GRCr8 |
| grcg7b | Chicken | bGalGal1.mat.broiler.GRCg7b |
| wbcel235 | Roundworm | WBcel235 |
| bdgp654 | Fruitfly | BDGP6.54 |
| grcz11 | Zebrafish | GRCz11 |
| mmul10 | Macaque | Mmul_10 |
| roscfam1 | Dog | ROS_Cfam_1.0 |
| sscrofa111 | Pig | Sscrofa11.1 |
Datasets are named after the genome assembly from now on, not the species.
A species-based name stops describing its own contents as soon as Ensembl switches assembly, and nothing fails to make that visible — the data simply changes underneath the name. Naming after the assembly means a stale name is obvious.
Eight datasets were renamed. The old names were removed rather than deprecated, so existing code errors instead of quietly returning a different assembly:
| Old | New | Species | Assembly |
|---|---|---|---|
| rnor6 | grcr8 | Rat | GRCr8 |
| grcm38 | grcm39 | Mouse | GRCm39 |
| galgal5 | grcg7b | Chicken | bGalGal1.mat.broiler.GRCg7b |
| mmul801 | mmul10 | Macaque | Mmul_10 |
| cfamiliaris | roscfam1 | Dog | ROS_Cfam_1.0 |
| bdgp6 | bdgp654 | Fruitfly | BDGP6.54 |
| drerio | grcz11 | Zebrafish | GRCz11 |
| sscrofa | sscrofa111 | Pig | Sscrofa11.1 |
This applies to the _tx2gene tables too. grch37, grch38 and wbcel235
were already assembly-named and are unchanged.
HTTP 405 Method Not Allowed from getBM(). www.ensembl.org
308-redirects BioMart to a GET-only endpoint, which rejects the POST biomaRt
uses to submit query XML.get_mart() constructs the Mart object directly and calls useDataset() on
it, instead of useMart(). The BioMart registry advertises
host="www.ensembl.org" for every mart, so useMart() would send its
dataset-list request to the broken host before returning; patching
mart@host afterwards was too late.data-raw/build_progress.log and skipped on rerun; the log is removed once
all tables are present."is not valid", "unavailable" and
"incompatible version". An overloaded archive serves an HTML error page with
HTTP 200, which biomaRt parses as data and misreports as a bad dataset name or
a version mismatch.options(timeout = 600). biomaRt uses R's 60s default, and a cold archive
host was measured taking 51.7s to return the registry alone.tx2gene no longer overwrites recipes in place.load_recipes globs *.yml only.data-raw/switch-host.sh and data-raw/recipes/README.md.