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CalCOFI integrated database release v2026.10.08

RELEASE_NOTES.md on gs://calcofi-db/ducklake/releases/v2026.10.08

Release date: 2026-10-08 · promoted (latest.txt)

The three marine mammal datasets are withdrawn until the lab that collected them has reviewed them

sio_cetacean-sightings, sio_cetacean-sonobuoy and sio_cetacean-edna entered in v2026.10.05 from CalCOFI/marmam-app, the copy a Shiny app was built on, with their licences and citations still being asked of the provider. We published before the Scripps Whale Acoustics Lab had reviewed them. Simone Baumann-Pickering (2026-10-07) explained that the app's data were exploratory, not the lab's final QA/QC'd product, that the lab had meant to hold marine mammal data until Michaela Alksne's density manuscript is submitted, and that the eDNA screens were generated by the Semmens team. All three are now in_release: false, so none of their rows is in this release:

  • sio_cetacean-sightings is being re-ingested from the QA/QC'd on-effort sightings and segments Michaela Alksne prepared, and returns only when the lab signs off on it, its licence and its citation.
  • sio_cetacean-sonobuoy waits until the lab identifies the product to distribute publicly.
  • sio_cetacean-edna waits on the Semmens team.

Their ingest notebooks are also off calcofi.io/workflows. The sample_type values (sighting, deployment, scan, water) and the measurement_type rows they introduced stay in the registry with no rows behind them; edna_presence is still filled by calcofi_2022-edna.

v2026.10.05 and v2026.10.06 are retired. They carried the marmam-app rows, so their parquet is removed (scripts/thin_releases.R --withdraw); nothing in them was rewritten. Their catalogs, sidecars, release notes and DOIs stay, and each retired.json names this release as the one to read instead.

Consumers: a query filtered on dataset_key LIKE 'sio_cetacean%' now returns no rows.

Contents (generated)

table rows
climatology 814,392 partitioned
cruise 845
dataset 19
dataset_taxon 1,940
fish 10,796
grid 225
grid_crosswalk 673
lookup 26
measurement_type 231
obs 33,324,138 deprecated → obs_bio, obs_env (objects removed in next)
obs_attribute 455,300
obs_bio 1,586,795
obs_env 31,737,343 partitioned
region 4
sample 1,467,016
sample_measurement 658,009
sample_spatial 927,600
ship 49
spatial 13,206
spatial_attribute 148,461
taxon 2,606
taxon_group 438
obs_ctd_full 281,880,519 supplemental
obs_mets_full 19,926,523 supplemental
sample_root 419,050 supplemental

25 tables, 373,376,204 rows, 2.73 GB.

Datasets (19): calcofi_2022-edna, calcofi_bottle, calcofi_ctd-cast, calcofi_ctd-derived, calcofi_dic, calcofi_mets, calcofi_phyllosoma, calcofi_phytoplankton, cce-lter_euphausiids, cce-lter_iron, cce-lter_picoplankton-bacteria, cce-lter_zoodb, cce-lter_zooscan, cdfw_dungeness-crab, farallon_bird-mammal, sio_mesopelagic-fish, sio_pic-zooplankton, swfsc_cufes, swfsc_ichthyo

Validation: 92 pass / 0 fail / 4 skip (consumer-contract suite, 2026-10-08T14:34:43Z).

Software: calcofi4db 4.22.0, calcofi4r 1.27.0.

How to cite

CalCOFI (2026). CalCOFI Integrated Database, release v2026.10.08 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://doi.org/10.5281/zenodo.23241748

Cite the source datasets you use alongside the release:

Access

con <- calcofi4r::cc_get_db(version = "v2026.10.08")

con = calcofi4py.cc_get_db("v2026.10.08")

Parquet: https://storage.googleapis.com/calcofi-db/ducklake/releases/v2026.10.08/parquet/{table}.parquet; full history: RELEASES.md.