Cetacean eDNA
CalCOFI Cetacean eDNA Detections (NCOG samples)
sio_cetacean-ednaSIOlicence pendingv2026.10.05validated
- years
- 2014–2016
- observations
- 497
- sampling events
- 71
- stations
- 21
- species
- 7
- depth
- 0–515 m
Overview
Cetacean species detections from environmental DNA (eDNA) in seawater samples collected by the NOAA CalCOFI Genomics Program (NCOG) at 10-40 m (a few deeper) on CalCOFI cruises, 2014-2016. Seven dolphin and whale species detected by metabarcoding: 1 = detected, 0 = not detected in a sequenced sample (a non-detection, not a confirmed absence). The 62 samples listed as “not sequenced, PCR negative” did not amplify, so they say nothing about any species: each stays a sample with no edna_presence rows (not a 0) until the provider says what a PCR negative means (Q04). Samples have no parent sample (each is a root event); the CalCOFI bottle each was filtered from is matched only as evidence of its time and cruise. Each sample is timed by its CTD-rosette bottle cast. Staged from the CalCOFI marine mammal Shiny app repository (CalCOFI/marmam-app).
Open with the provider
- Q01 license — open
- Q02 citation_main — open
- Q03 pi_names — proposed
Coverage
1 variable
obs_bio profile · one value per taxon at a sampling event · 497 values · 2014–2016 · 1 variable
Species and taxa
- Megaptera novaeangliae Humpback Whale 71
- Delphinus delphis Short-Beaked Common Dolphin 71
- Grampus griseus Risso's Dolphin 71
- Tursiops truncatus Bottlenose Dolphin 71
- Sagmatias obliquidens Pacific White-Sided Dolphin 71
- Lissodelphis borealis Northern Right Whale Dolphin 71
- Delphinus capensis Long-beaked Common Dolphin 71
Access
Every endpoint this dataset can be reached through, grouped by how you would use it. Each name is the link; the copy button beside it copies the address. Everything is in the release record and was answered when the release was cut.
Apps that read this dataset from the release. The icons after a name are the app’s lenses — the spatial grain it shows the data at.
Every way to have the bytes, by source. Nothing here asks you to register first.
Tables from the release (Parquet)
The release’s own tables, as the parquet objects it is frozen from — the same bytes every app and package below reads. A table this dataset shares with others holds every dataset’s rows, so filter on dataset_key; a partition holds only this dataset’s. since is the release whose rows these are: an unchanged table keeps its object.
From the provider
The dataset as its provider publishes it, before CalCOFI ingested it.
The same release, from a script or a browser SQL shell.
Packages
The whole release, pinned to a version, with the citation one call away.
con <- calcofi4r::cc_get_db()
calcofi4r::cc_cite("sio_cetacean-edna")con = calcofi4py.cc_get_db()
calcofi4py.cc_cite("sio_cetacean-edna")DuckDB, anywhere
No CalCOFI package needed: each table above is a plain parquet object, readable by any DuckDB (or Arrow, pandas, Spark) from its URL. The path carries a content hash — a table whose rows did not change between releases keeps the same object, so nothing unchanged is stored or downloaded twice. Swap in any table above; one shared with other datasets needs WHERE dataset_key = 'sio_cetacean-edna'. Every object of every release is listed in db-schema.
SELECT *
FROM read_parquet('https://storage.googleapis.com/calcofi-db/ducklake/tables/obs/dataset_key=sio_cetacean-edna/ccdb631db5874f4e12a93f88/data_0.parquet')
LIMIT 100;db-query, in the browser
__TBL:obs__ is db-query’s name for the pinned release’s obs object — the hashed path above, resolved for you — so the same SQL keeps working when a release changes the object.
-- sio_cetacean-edna in the CalCOFI release v2026.10.05
SELECT *
FROM __TBL:obs__
WHERE dataset_key = 'sio_cetacean-edna'
LIMIT 100;Records about the data, in the standards each portal harvests.
Where this dataset is registered outside calcofi.io: each portal’s role, what it is for, the dataset’s status there and the identifier it is known by. The policy — which portal is the archive of record and why — is in Portals.
Policy Archive of record: none known; not the calpoly_whale-edna Zenodo deposit.
Everything here is open — nothing on calcofi.io asks you to register first. If this dataset ends up in something you build or publish, register your use so it can be credited and linked back; to hear when a release changes it, stay informed. Questions: data@calcofi.io.
Cite
This dataset's own citation. What to cite, and how, is a chapter of the docs book.
The provider has not confirmed a citation for this dataset yet. Cite the release below, and name the dataset by its key.
CalCOFI Cetacean eDNA Detections (NCOG samples) [dataset].
License: not yet establishedBibTeX
@misc{sio_cetacean-edna,
title = {CalCOFI Cetacean eDNA Detections (NCOG samples)},
note = {License: not yet established}
}…and the release it came from
CalCOFI (2026). CalCOFI Integrated Database, release v2026.10.05 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://calcofi.io/db-schema/?v=v2026.10.05BibTeX
@misc{calcofi_release_v2026_10_05,
title = {CalCOFI Integrated Database, release v2026.10.05},
author = {CalCOFI},
year = {2026},
publisher = {Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife},
url = {https://calcofi.io/db-schema/?v=v2026.10.05}
}Source files
The original inputs the ingest notebook read, archived by the ingest to the public files bucket — 1 file, 16.4 KB.
- edna.csv16.4 KB2026-10-04