ZooDB (Holoplankton Community)
ZooDB Holoplankton Community
cce-lter_zoodbCCE-LTERCustom terms stated by the providerv2026.09.05metadata
- years
- 1951–2015
- observations
- 30,948
- sampling events
- 506
- stations
- 54
- taxa
- 33
- depth
- 0–225 m
Overview
Holoplankton abundance and carbon biomass by 33 higher taxa (copepods to family, plus amphipods, chaetognaths, salps, pyrosomes, pteropods, ostracods, foraminifera, radiolaria and more) from CalCOFI net tows, 1951-2021, enumerated by microscopy (Ohman Lab / SIO Pelagic Invertebrate Collection). One row per (sample, taxon, measurement_type); unpooled tows are station-resolved, pooled samples are per-cruise regional composites. Raw (uncorrected) abundance per 1000 m3 and per m2, plus biomass mg C/m2.
Open with the provider
- Q10 citation_main — proposed
calcofi.org page ↗source ↗ingest notebook ↗record JSON JSON-LD
Access
Every endpoint this dataset can be reached through, grouped by how you would use it. Every URL is in the release record and answered when the release was cut.
Explore
Apps that read this dataset from the release. A row marked “this dataset” opens with it already selected.
https://calcofi.io/explore/?datasets=cce-lter_zoodb
https://app.calcofi.io/station/?dataset=cce-lter_zoodb
https://app.calcofi.io/hex/?datasets=cce-lter_zoodb
https://app.calcofi.io/cruise/?datasets=cce-lter_zoodb
https://calcofi.io/2026-ucsb-station-data-portal/
Query
SQL against the release itself, in the browser — nothing to install and nothing downloaded until a query asks for it. __TBL:obs__ resolves to the pinned release’s parquet.
-- cce-lter_zoodb in the CalCOFI release v2026.09.05
SELECT *
FROM __TBL:obs__
WHERE dataset_key = 'cce-lter_zoodb'
LIMIT 100;https://calcofi.io/db-query/?sql=--+cce-lter_zoodb+in+the+CalCOFI+release+v2026.09.05%0ASELECT+%2A%0AFROM+__TBL%3Aobs__%0AWHERE+dataset_key+%3D+%27cce-lter_zoodb%27%0ALIMIT+100%3B#sql-shell--shell
Code
The same release, from a script.
con <- calcofi4r::cc_get_db()
calcofi4r::cc_cite("cce-lter_zoodb")con = calcofi4py.cc_get_db()
calcofi4py.cite("cce-lter_zoodb")SELECT * FROM read_parquet('https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_zoodb/eea6422d45a7ccd2ebbe37a6/data_0.parquet') LIMIT 100;Get the data
Every way to have the bytes, by source. Nothing here asks you to register first.
Files from the release (Parquet)
The frozen objects this release is made of. A partition holds only this dataset’s rows; a shared table holds every dataset’s, so filter on dataset_key.
https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_zoodb/eea6422d45a7ccd2ebbe37a6/data_0.parquet
CF netCDF
One self-describing file, for a tool that reads netCDF.
how far this file is CF
Fully CF: each row is an independent observation with its own time and position, which is a CF point collection. Rows are at the OCCURRENCE grain (event x taxon x life stage x depth), not the event grain, so a sample with many taxa contributes many points.
https://storage.calcofi.io/calcofi-files-public/netcdf/cce-lter_zoodb/v2026.09.04/cce-lter_zoodb.nc
ERDDAP (erddap.calcofi.io)
One ERDDAP dataset per grain, each with its own data formats and its own pages. Subset in the browser or query it from a script.
- observations
- one row per measurement, joined to the event it was taken on
- sampling events
- one row per cast, tow or transect — when, where and how it was sampled
From the provider
The dataset as its provider publishes it, before CalCOFI ingested it.
https://oceaninformatics.ucsd.edu/zoodb/
Metadata records
Records about the data, in the standards each portal harvests.
https://erddap.calcofi.io/erddap/metadata/iso19115/xml/cce-lter_zoodb_iso19115.xml
https://erddap.calcofi.io/erddap/metadata/fgdc/xml/cce-lter_zoodb_fgdc.xml
https://calcofi.io/datasets/cce-lter_zoodb.jsonld
https://calcofi.io/datasets/cce-lter_zoodb.json
https://calcofi.io/data.json
https://calcofi.io/stac/#/collections/cce-lter_zoodb/collection.json
Archives & portals
Where this dataset is registered outside calcofi.io, by the identifier each portal knows it as.
https://erddap.calcofi.io/erddap/info/cce-lter_zoodb/index.html
https://doi.org/10.5281/zenodo.22281994
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
The provider has not confirmed a citation for this dataset yet. Cite the release below, and name the dataset by its key.
ZooDB Holoplankton Community [dataset].
License: custom (https://oceaninformatics.ucsd.edu/zoodb/)
Acknowledgement: Plankton sample analysis supported by NSF grants to M.D. Ohman and the CCE-LTER site, and by the SIO Pelagic Invertebrate Collection.BibTeX
@misc{cce-lter_zoodb,
title = {ZooDB Holoplankton Community},
note = {License: custom (https://oceaninformatics.ucsd.edu/zoodb/); Acknowledgement: Plankton sample analysis supported by NSF grants to M.D. Ohman and the CCE-LTER site, and by the SIO Pelagic Invertebrate Collection.}
}Acknowledgement. Plankton sample analysis supported by NSF grants to M.D. Ohman and the CCE-LTER site, and by the SIO Pelagic Invertebrate Collection.
…and the release it came from
CalCOFI (2026). CalCOFI Integrated Database, release v2026.09.05 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://calcofi.io/db-schema/?v=v2026.09.05BibTeX
@misc{calcofi_release_v2026_09_05,
title = {CalCOFI Integrated Database, release v2026.09.05},
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=v2026.09.05}
}