2022 Vertebrate eDNA

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.

con <- calcofi4r::cc_get_db()
calcofi4r::cc_cite("calcofi_2022-edna")

con = calcofi4py.cc_get_db()
calcofi4py.cc_cite("calcofi_2022-edna")

SELECT *
FROM read_parquet('https://storage.googleapis.com/calcofi-db/ducklake/tables/obs/dataset_key=calcofi_2022-edna/f4bd530899502d593fd4a585/data_0.parquet')
LIMIT 100;

SELECT *
FROM read_parquet('https://storage.googleapis.com/calcofi-db/ducklake/tables/sample_measurement/8886d18848f51b6bce70f01d/sample_measurement.parquet')
WHERE dataset_key = 'calcofi_2022-edna'
LIMIT 100;

-- calcofi_2022-edna in the CalCOFI release v2026.10.21
SELECT *
FROM __TBL:obs__
WHERE dataset_key = 'calcofi_2022-edna'
LIMIT 100;

This dataset's own citation. What to cite, and how, is a chapter of the docs book.

Patin N, ODonnell G (2026). CalCOFI October 2022 Vertebrate eDNA. Version 1.3. Occurrence dataset. https://doi.org/10.15468/n52j6r

License: CC-BY-4.0
DOI: https://doi.org/10.15468/n52j6r
Acknowledgement: This work was made possible by the Office of Naval Research Multidisciplinary University Research Initiative (MURI) funding for MMARINeDNA (award no.: N00014-22-1-2719) with additional support from the National Science Foundation (award no.: OCE-2224726). It includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (no.: S10 OD026929). We thank the captain and crew of the NOAA Ship Reuben Lasker, Rachel Pound from CalCOFI and Harrison Huang and Dylan Inskeep from the California Department of Fish and Wildlife for their assistance with sample collection.

@misc{calcofi_2022-edna,
  title        = {CalCOFI October 2022 Vertebrate eDNA},
  howpublished = {Patin N, ODonnell G (2026). CalCOFI October 2022 Vertebrate eDNA. Version 1.3. Occurrence dataset. https://doi.org/10.15468/n52j6r
},
  year         = {2026},
  doi          = {10.15468/n52j6r},
  url          = {https://doi.org/10.15468/n52j6r},
  note         = {License: CC-BY-4.0; Acknowledgement: This work was made possible by the Office of Naval Research Multidisciplinary University Research Initiative (MURI) funding for MMARINeDNA (award no.: N00014-22-1-2719) with additional support from the National Science Foundation (award no.: OCE-2224726). It includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (no.: S10 OD026929). We thank the captain and crew of the NOAA Ship Reuben Lasker, Rachel Pound from CalCOFI and Harrison Huang and Dylan Inskeep from the California Department of Fish and Wildlife for their assistance with sample collection.
}
}

Acknowledgement. This work was made possible by the Office of Naval Research Multidisciplinary University Research Initiative (MURI) funding for MMARINeDNA (award no.: N00014-22-1-2719) with additional support from the National Science Foundation (award no.: OCE-2224726). It includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (no.: S10 OD026929). We thank the captain and crew of the NOAA Ship Reuben Lasker, Rachel Pound from CalCOFI and Harrison Huang and Dylan Inskeep from the California Department of Fish and Wildlife for their assistance with sample collection.

…and the release it came from

CalCOFI (2026). CalCOFI Integrated Database, release v2026.10.21 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://calcofi.io/db-schema/?v=v2026.10.21

@misc{calcofi_release_v2026_10_21,
  title     = {CalCOFI Integrated Database, release v2026.10.21},
  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=v2026.10.21}
}

source accessed

2026-10-21

record updated

2026-10-01

release tables

sampleobssample_measurementtaxondataset_taxonmeasurement_type

blockers

Un-held 2026-10-04 (Ben): ships in the next release as detections only (edna_presence = 1 and read counts; the archive holds positive detections only, so no row is not a non-detection). Q08 (omitted zero-detection runs) stays open, now high; Q07 (read filtering, controls) and Q06 (ASV/PCR-replicate summing) stay open. 2026-10-01 rework of PR #118 (review decision B4): obs = one row per filter x taxon x measurement_type -- edna_presence (shared with sio_cetacean-edna; 1 only, positive detections) + edna_reads_dloop / edna_reads_12s (reads summed over ASVs and PCR replicates); no obs_attribute; sample_key calcofi_2022-edna:filter:<parentEventID>; sample_measurement carries nutrients/chl_fluor/oxygen_mg_l/dna_concentration + per-assay raw and filtered read totals; 'OTUs or ASVs assigned to taxa' held back (Q04: equals the summed reads). Rendered + uploaded to gs://calcofi-db/ingest/calcofi_2022-edna/ 2026-10-01: sample 47 / obs 148 / sample_measurement 482. site_key/parent_sample_key NULL pending Q05.

What changed in v2026.10.21

• obs 5.7 KB · since v2026.10.05
• sample_measurement 2.5 MB · since v2026.10.21

Source files

The original inputs the ingest notebook read, archived by the ingest to the public files bucket — 4 files, 378 KB.

• 0005456-260916113435855.zip9.9 KB2026-10-01
• _archive/dwca-calcofi_october2022_edna-v1.2.zip124 KB2026-10-21
• dwca-calcofi_october2022_edna-v1.2.zip124 KB2026-10-01
• dwca-calcofi_october2022_edna-v1.3.zip121 KB2026-10-21

release changelog ↗

eDNAmetabarcodingdolphinsrare targets