https://calcofi.io/datasets/cce-lter_zoodb/ ZooDB (Holoplankton Community) Mark D. Ohman UCSD SIO mohman@ucsd.edu Moira Decima UCSD SIO 2026-10-21 eng 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. EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > ZOOPLANKTON EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > COPEPODS GCMD Science Keywords Zooplankton Biomass and Diversity Zooplankton zooplankton_abundance count/1000m3 zooplankton_abundance_areal count/m2 zooplankton_biomass_carbon mgC/m2 This work is licensed under a Custom terms stated by the provider. https://calcofi.io/datasets/cce-lter_zoodb/ 30.8–37.6°N, 125.8–117.3°W -125.78 -117.3 37.62 30.75 1951 2015 Zooplankton family Aetideidae COPEPODA CALANOIDA AETIDEIDAE 104075 class Appendicularia APPENDICULARIA 146421 family Atlantidae atlantas 22990 family Calanidae COPEPODA CALANOIDA CALANIDAE 104079 order Calanoida COPEPODA OTHER CALANOIDS 1100 family Candaciidae COPEPODA CALANOIDA CANDACIIDAE 104080 phylum Chaetognatha arrow worms 2081 class Copepoda copepods 1080 phylum Ctenophora Comb jelly 1248 order Doliolida DOLIOLIDA 137212 family Eucalanidae COPEPODA CALANOIDA EUCALANIDAE 104085 family Euchaetidae COPEPODA CALANOIDA EUCHAETIDAE 104086 suborder Euthecosomata MOLLUSCA EUTHECOSOMATA 23020 phylum Foraminifera foraminiferans 1410 family Galatheidae squat lobsters 106733 suborder Gammaridea AMPHIPODA GAMMARIDEA 1207 suborder Gymnosomata naked pteropods 164 family Heterorhabdidae COPEPODA CALANOIDA HETERORHABDIDAE 104087 class Hydrozoa hydrozoans 1337 suborder Hyperiidea AMPHIPODA HYPERIIDEA 1205 family Lucicutiidae COPEPODA CALANOIDA LUCICUTIIDAE 104088 family Metridinidae COPEPODA CALANOIDA METRIDINIDAE 104092 class Ostracoda ostracods 1078 family Pasiphaeidae glass shrimps 106790 family Pontellidae COPEPODA CALANOIDA PONTELLIDAE 104097 suborder Pseudothecosomata MOLLUSCA PSEUDOTHECOSOMATA 23021 order Pyrosomatida PYROSOMA 137213 phylum Radiozoa radiolarians 582421 order Salpida Salp 137214 family Scolecitrichidae COPEPODA CALANOIDA SCOLECITRICHIDAE 104103 superfamily Sergestoidea DECAPODA SERGESTOIDEA 106684 order Siphonophorae Siphonophore 1371 family Tomopteridae POLYCHAETA TOMOPTERIDAE 958 Irregular; ongoing California Current Ecosystem Long Term Ecological Research mohman@ucsd.edu QC flags present: No. Mark D. Ohman UCSD SIO mohman@ucsd.edu lead Moira Decima UCSD SIO lead NSF sample One row per physical sampling event at its native grain (site, tow, net, subsample, cast, bottle, water, filter, underway, transect, sighting, deployment, scan, region pool). An adjacency list: parent_sample_key points at the containing event and root_sample_key at the top of the chain, so counting distinct events at any level is a single GROUP BY. sample_key Sample Key Globally unique event key, namespaced dataset_key:sample_type:id so the same integer id in two datasets — or at two event levels in one dataset — never collides. VARCHAR Globally unique event key, namespaced dataset_key:sample_type:id so the same integer id in two datasets — or at two event levels in one dataset — never collides. sample_type Sample Type Event grain: site, tow, net, subsample, cast, bottle, water (an eDNA water sample), filter (an eDNA water filter), underway, transect (a visual-survey effort segment), sighting, deployment (a sonobuoy), scan (one analysed hour of a recording) or region_pool. VARCHAR Event grain: site, tow, net, subsample, cast, bottle, water (an eDNA water sample), filter (an eDNA water filter), underway, transect (a visual-survey effort segment), sighting, deployment (a sonobuoy), scan (one analysed hour of a recording) or region_pool. parent_sample_key Parent Sample Key The containing event (net → tow → site; bottle → cast; sighting → transect; scan → deployment). NULL at the top of the chain. Flat adjacency list: attributes are not inherited. VARCHAR The containing event (net → tow → site; bottle → cast; sighting → transect; scan → deployment). NULL at the top of the chain. Flat adjacency list: attributes are not inherited. root_sample_key Root Sample Key Top of this event's containment chain; equals sample_key for single-level datasets. Use count(DISTINCT root_sample_key) to count stations/casts irrespective of grain. VARCHAR Top of this event's containment chain; equals sample_key for single-level datasets. Use count(DISTINCT root_sample_key) to count stations/casts irrespective of grain. dataset_key Dataset Key Provenance stamp: provider_dataset. VARCHAR Provenance stamp: provider_dataset. grid_key Grid Key CalCOFI station grid cell. NULL where the dataset has no station assignment (region-pooled phytoplankton). VARCHAR CalCOFI station grid cell. NULL where the dataset has no station assignment (region-pooled phytoplankton). site_key Site Key CalCOFI station natural key as the source records it (line/station, e.g. 090.0 060.0). Present on 13 of the 18 source event tables, so it is carried on the event dimension rather than lost to consolidation; grid_key is the derived grid cell, this is the source's own station id. VARCHAR CalCOFI station natural key as the source records it (line/station, e.g. 090.0 060.0). Present on 13 of the 18 source event tables, so it is carried on the event dimension rather than lost to consolidation; grid_key is the derived grid cell, this is the source's own station id. cruise_key Cruise Key CalCOFI cruise natural key YYYY-MM-NODC. VARCHAR CalCOFI cruise natural key YYYY-MM-NODC. order_occ Order of Occupation Order in which the station was occupied on the cruise. Source spelling varies (order_occ, ord_occ) and CTD stores it as text; normalised to an integer here. INTEGER dimensionless integer latitude Latitude Event latitude (WGS84). DOUBLE degree real longitude Longitude Event longitude (WGS84). DOUBLE degree real datetime Datetime Event start time (UTC). TIMESTAMP YYYY-MM-DDThh:mm:ss depth_min_m Depth Min Shallowest depth sampled by this event. DOUBLE meter real depth_max_m Depth Max Deepest depth sampled by this event; for swfsc_ichthyo tows and nets the maximum possible depth of the net (SWFSC Net.NetDepth, nominal: over a shallower sea floor the net did not reach it). DOUBLE meter real tow_type Tow Type Net gear code where the dataset records one (C1/CB/CV/PV oblique or vertical, MT manta); NULL for gears and datasets without one. Needed to compute gear-appropriate CPUE. VARCHAR Net gear code where the dataset records one (C1/CB/CV/PV oblique or vertical, MT manta); NULL for gears and datasets without one. Needed to compute gear-appropriate CPUE. data_stage Data Stage The source's own processing state for this event: final (post-cruise calibrations applied) or preliminary (not for publication — the source warns that oxygen, nitrate and chlorophyll may change significantly once calibrated). Populated by calcofi_ctd-cast; NULL where the dataset draws no such distinction, which is not a claim that the data are final. VARCHAR The source's own processing state for this event: final (post-cruise calibrations applied) or preliminary (not for publication — the source warns that oxygen, nitrate and chlorophyll may change significantly once calibrated). Populated by calcofi_ctd-cast; NULL where the dataset draws no such distinction, which is not a claim that the data are final. geom Geometry Point geometry minted from longitude/latitude (OGC:CRS84). GEOMETRY('EPSG:4326') Point geometry minted from longitude/latitude (OGC:CRS84). source_uuid Source Uuid Source Uuid UUID Source Uuid hex7 H3 Cell (res 7) One UBIGINT H3 cell at resolution 7: the parent of the resolution-10 cell of this event's own latitude / longitude (not the resolution-7 cell the position falls in), defined exactly as obs_bio.hex7 / obs_env.hex7; NULL without a finite position. Lets a per-sample value in sample_measurement be drawn in hexagons. An observation carries its own position, so a CTD scan can sit in another cell than its cast. UBIGINT dimensionless whole seafloor_depth_m seafloor_depth_m DOUBLE dimensionless real station_uuid station_uuid UUID station_uuid station_uuid_method station_uuid_method VARCHAR station_uuid_method obs The occurrence-headline long table: one scalar measurement per row, environmental (realm = 'env') and biological (realm = 'bio') together. Biological taxon is the global taxon_key; sub-occurrence detail (length/stage bins, behavior) lives in obs_attribute, and event-level effort in sample_measurement. data_0.parquet 158393 aa02a816aeb7110dd96e9299250f8a9ba910cf4058b574e8dfe4ff54de8b7c2e Apache Parquet https://storage.googleapis.com/calcofi-db/ducklake/tables/obs/dataset_key=cce-lter_zoodb/ec8222662276a4d489f21c97/data_0.parquet obs_id Observation ID Surrogate key, renumbered globally when the release concatenates the per-dataset shards. BIGINT dimensionless integer realm Realm env for physical/chemical measurements, bio for organism observations. VARCHAR env for physical/chemical measurements, bio for organism observations. dataset_key Dataset Key Provenance stamp: provider_dataset. VARCHAR Provenance stamp: provider_dataset. sample_key Sample Key The sampling event this observation came from; joins sample. VARCHAR The sampling event this observation came from; joins sample. grid_key Grid Key CalCOFI station grid cell, denormalized from sample so rollups need no join. NULL for region-pooled data. VARCHAR CalCOFI station grid cell, denormalized from sample so rollups need no join. NULL for region-pooled data. cruise_key Cruise Key Cruise, denormalized from sample so rollups need no join. VARCHAR Cruise, denormalized from sample so rollups need no join. latitude Latitude Observation latitude (WGS84). DOUBLE degree real longitude Longitude Observation longitude (WGS84). DOUBLE degree real datetime Datetime Observation time (UTC). NULL for region-pooled data with no event time. TIMESTAMP YYYY-MM-DDThh:mm:ss depth_min_m Depth Min Shallowest depth this observation represents. DOUBLE meter real depth_max_m Depth Max Deepest depth this observation represents; equal to depth_min_m for point measurements (bottle, CTD scan). DOUBLE meter real taxon_key Taxon Key Global taxon key, worms:<AphiaID> or itis:<TSN> for birds. NULL for env rows. Joins taxon. VARCHAR Global taxon key, worms:<AphiaID> or itis:<TSN> for birds. NULL for env rows. Joins taxon. life_stage Life Stage Life stage where the source resolves one (larva, adult, juvenile, egg, phyllosoma). VARCHAR Life stage where the source resolves one (larva, adult, juvenile, egg, phyllosoma). measurement_type Measurement Type Measured quantity; joins the measurement_type vocabulary. VARCHAR Measured quantity; joins the measurement_type vocabulary. measurement_value Measurement Value The measured value, in the units measurement_type declares. DOUBLE dimensionless real measurement_qual Measurement Qualifier Source quality flag, verbatim. VARCHAR Source quality flag, verbatim. measurement_prec Measurement Precision Source-reported precision where available. DOUBLE dimensionless real hex_id Hex ID H3 cell at resolution 10, stored as UBIGINT. Aggregate coarser at query time with h3_cell_to_parent(hex_id, res) — there is no per-resolution column ladder. UBIGINT dimensionless whole taxon Taxonomic hierarchy for species via WoRMS and ITIS authorities (built from spp.duckdb via recursive CTEs) taxon_key Taxon Key Global taxon key: lowercase authority prefix plus id, worms:127023 or itis:176754. VARCHAR Global taxon key: lowercase authority prefix plus id, worms:127023 or itis:176754. worms_id WoRMS ID WoRMS AphiaID. INTEGER dimensionless integer itis_id ITIS ID ITIS Taxonomic Serial Number. INTEGER dimensionless integer gbif_id GBIF ID GBIF backbone taxon key. INTEGER dimensionless integer ncbi_id NCBI ID NCBI Taxonomy id. INTEGER dimensionless integer inat_id iNaturalist ID iNaturalist taxon id. INTEGER dimensionless integer scientific_name Scientific Name Accepted scientific name. VARCHAR Accepted scientific name. common_name Common Name Common name where one is recorded. VARCHAR Common name where one is recorded. rank Rank Taxonomic rank. VARCHAR Taxonomic rank. rank_order Rank Order Ordinal for sorting ranks from kingdom down. INTEGER dimensionless integer taxonomic_status Taxonomic Status Status as fetched from the keying authority (accepted, unaccepted, superseded combination, ...). Read it with status_checked — before v2026.08.05 this column was the literal string "accepted" on every row, stamped rather than fetched. VARCHAR Status as fetched from the keying authority (accepted, unaccepted, superseded combination, ...). Read it with status_checked — before v2026.08.05 this column was the literal string "accepted" on every row, stamped rather than fetched. status_checked Status Checked Date taxonomic_status was last confirmed against the authority. A status with no check date is not a fact. VARCHAR Date taxonomic_status was last confirmed against the authority. A status with no check date is not a fact. parent_taxon_key Parent Taxon Key Lineage parent; walk this to expand a taxon to its descendants. VARCHAR Lineage parent; walk this to expand a taxon to its descendants. kingdom Kingdom Kingdom. VARCHAR Kingdom. phylum Phylum Phylum. VARCHAR Phylum. class Class Class. VARCHAR Class. order_taxon Order Order (named order_taxon because order is a SQL keyword). VARCHAR Order (named order_taxon because order is a SQL keyword). family Family Family. VARCHAR Family. notes Notes Append-only provenance log, one datestamped line per entry: how each id was resolved and any re-key onto an authority-accepted id (e.g. itis:174553 Puffinus griseus -> itis:1255050 Ardenna grisea). The dataset's own original code and name stay in dataset_taxon. VARCHAR Append-only provenance log, one datestamped line per entry: how each id was resolved and any re-key onto an authority-accepted id (e.g. itis:174553 Puffinus griseus -> itis:1255050 Ardenna grisea). The dataset's own original code and name stay in dataset_taxon. dataset_taxon Crosswalk from each dataset's own taxon vocabulary to the global taxon_key. obs resolves its taxon by joining this on (dataset_key, ds_taxa_code), so a dataset can keep its local codes without leaking them into the shared model. ds_taxon_key Dataset Taxon Key Key of this crosswalk row, <dataset-or-known-list>:<local code>. VARCHAR Key of this crosswalk row, <dataset-or-known-list>:<local code>. dataset_key Dataset Key The dataset whose vocabulary this row belongs to. VARCHAR The dataset whose vocabulary this row belongs to. taxon_key Taxon Key The global taxon it resolves to; joins taxon. VARCHAR The global taxon it resolves to; joins taxon. ds_scientific_name Dataset Scientific Name Scientific name as the source dataset spells it. VARCHAR Scientific name as the source dataset spells it. ds_common_name Dataset Common Name Common name as the source dataset spells it. VARCHAR Common name as the source dataset spells it. ds_taxa_code Dataset Taxa Code The dataset's own code, as stored on its measurement rows. VARCHAR The dataset's own code, as stored on its measurement rows. ds_source_json Ds Source Json Ds Source Json VARCHAR Ds Source Json measurement_type measurement_type Measurement Type Measurement Type VARCHAR Measurement Type description Description Description VARCHAR Description units Units Units VARCHAR Units valid_min Valid Min Valid Min DOUBLE dimensionless real valid_max Valid Max Valid Max DOUBLE dimensionless real valid_depth_min_m Valid Depth Min M Valid Depth Min M DOUBLE dimensionless real valid_depth_max_m Valid Depth Max M Valid Depth Max M DOUBLE dimensionless real derivation Derivation Derivation VARCHAR Derivation is_canonical Is Canonical Is Canonical BOOLEAN Is Canonical _source_column Source Column Source Column VARCHAR Source Column _source_table Source Table Source Table VARCHAR Source Table _source_datasets Source Datasets Source Datasets VARCHAR Source Datasets _qual_column Qual Column Qual Column VARCHAR Qual Column _prec_column Prec Column Prec Column VARCHAR Prec Column grain Grain Grain VARCHAR Grain denominator Denominator Denominator VARCHAR Denominator category Category Category VARCHAR Category variable Variable Variable VARCHAR Variable nerc_p01 Nerc P01 Nerc P01 VARCHAR Nerc P01 units_nerc_p06 Units Nerc P06 Units Nerc P06 VARCHAR Units Nerc P06 provider Provider Provider VARCHAR Provider dataset Dataset Dataset VARCHAR Dataset Plankton sample analysis supported by NSF grants to M.D. Ohman and the CCE-LTER site, and by the SIO Pelagic Invertebrate Collection. cce-lter_zoodb https://calcofi.io/datasets/cce-lter_zoodb/ v2026.10.21 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 2026-10-21