# CalCOFI integrated database release 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## The three marine mammal datasets are withdrawn until the lab that collected them has reviewed them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:

- `calcofi_2022-edna` — Patin N, ODonnell G (2026). CalCOFI October 2022 Vertebrate eDNA. Version 1.2. Occurrence dataset. https://doi.org/10.15468/n52j6r
 · CC-BY-4.0
- `calcofi_bottle` — CalCOFI. (2023). CalCOFI Bottle Database 194903-202105. CalCOFI.org. · *license pending*
- `calcofi_ctd-cast` — CalCOFI. (2023). CalCOFI CTD Cast Files. CalCOFI.org. · *license pending*
- `calcofi_ctd-derived` — CalCOFI. (2026). CalCOFI CTD Derived Hydrographic Products (from the CalCOFI CTD Cast Files). CalCOFI.io. https://calcofi.io/workflows/ingest_calcofi_ctd-derived.html · *license pending*
- `calcofi_dic` — Keeling, C.D.; Lueker, T.J.; Emanuele, G.; Dickson, A.G.; Martz, T.R.; Wolfe, W.H.; Mau, A. (2025). Discrete profile dissolved inorganic carbon, total alkalinity, water temperature and salinity measurements for CalCOFI (NCEI Accession 0301029). NOAA NCEI. https://doi.org/10.25921/3w9f-jd72 · CC-BY-4.0
- `calcofi_mets` — CalCOFI. Underway (METS) TSG/Meteorology Data. CalCOFI.org. · *license pending*
- `calcofi_phyllosoma` — CalCOFI - Scripps Institution of Oceanography and T. Koslow. 2017. Data pertaining to lobster phyllosoma, Panulirus interruptus, collection methods, locations, identification and staging (1951-2008, months of July and August) ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/9e38121ebb26f1b59b7b39b2eff844fa · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.188.4)
- `calcofi_phytoplankton` — CalCOFI - Scripps Institution of Oceanography, California Current Ecosystem LTER, and E. Venrick. 2023. Temporal and spatial changes of the abundance and species composition of phytoplankton in the California Current from samples collected aboard CalCOFI cruises from summer 1996 through 2022. ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/60edabfbfd85c623fce05822befaa071 · CC0-1.0 (https://creativecommons.org/publicdomain/zero/1.0/)
- `cce-lter_euphausiids` — Ohman, M.D. 2022. California Current Ecosystem Euphausiid data, Brinton and Townsend Euphausiid Database (BTEDB) ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/4a92a0044bcd1523a4f994ece874a57d · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.313.1)
- `cce-lter_iron` — California Current Ecosystem LTER, CalCOFI - Scripps Institution of Oceanography, and K. Barbeau. 2017. Measurements of dissolved inorganic concentrations of nutrient iron and of iron limitation at selected stations and depths from CalCOFI cruises in the California Current System, Nov. 2002 - July 2004 (completed) ver 3. Environmental Data Initiative. https://doi.org/10.6073/pasta/63c4e57f87861db3acaf80d1dec103e1.
 · custom (https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.21.3)
- `cce-lter_picoplankton-bacteria` — Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER. · *license pending*
- `cce-lter_zoodb` — *citation pending* · custom (https://oceaninformatics.ucsd.edu/zoodb/)
- `cce-lter_zooscan` — *citation pending* · custom (https://oceaninformatics.ucsd.edu/zooscandb/)
- `cdfw_dungeness-crab` — Rogers-Bennett, L.; Jones, E.; Klemmedson, A. (2026). CDFW Dungeness Crab Megalopae from archived CalCOFI plankton samples (1949-2014). California Department of Fish and Wildlife, published through CalCOFI / Scripps Institution of Oceanography.
 · CC-BY-4.0
- `farallon_bird-mammal` — *citation pending* · custom (https://oceanview.pfeg.noaa.gov/CalCOFI/app/resources/docs/Data_Sharing_Agreement_FarallonInstitute.pdf)
- `sio_mesopelagic-fish` — Koslow, J. Anthony (2016). CalCOFI Trawl Data. In California Cooperative Oceanic Fisheries Investigations (CalCOFI): Acoustic and Trawl Data. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0BZ64DH
 · CC-BY-4.0
- `sio_pic-zooplankton` — *citation pending* · *license pending*
- `swfsc_cufes` — *citation pending* · custom (https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIcufes.das)
- `swfsc_ichthyo` — NOAA Fisheries SWFSC. CalCOFI Ichthyoplankton Database. · *license pending*

## Access

```r
con <- calcofi4r::cc_get_db(version = "v2026.10.08")
```
```python
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](https://storage.googleapis.com/calcofi-db/ducklake/releases/RELEASES.md).