CalCOFI Workflows

Ingest Bottle Database

Hydrographic bottle data including temperature, salinity, oxygen, nutrients, pigments, and C14 from CalCOFI cruises.

Ingest CalCOFI Bird & Mammal Census

Bird and mammal observations along CalCOFI (and NMFS, CPR) cruise transects, 1987-2021. Transect effort + counts + species/behavior lookups. Curated via CCE-LTER DataZoo 255 (PI Bill Sydeman).

Ingest CalCOFI CTD Cast Data

CTD downcast profiles with temperature, salinity, oxygen, fluorescence, and other sensors at standard depths.

Ingest CalCOFI Lobster Phyllosoma

Spiny lobster (Panulirus interruptus) phyllosoma larvae counts by developmental stage from CalCOFI net tows, 1951-2008. Source: EDI knb-lter-cce.188.4 (Koslow).

Ingest CalCOFI Phytoplankton (Venrick)

Abundance and species composition of phytoplankton (385 taxonomic categories) in the California Current, 1996-2022, by inverted-microscope counts (E. Venrick). Samples from the near-surface "second depth" are pooled across stations into four regions (NE, SE, Alley, Offshore; Hayward & Venrick 1998) before counting, so the grain is cruise x region, not per-station. Source: EDI knb-lter-cce.254.4.

Ingest DIC

Discrete profile dissolved inorganic carbon (DIC) and total alkalinity (TA) from CalCOFI Niskin bottle samples, quality-controlled using WOCE flagging.

Ingest Spatial Boundaries

Ingest NOAA CalCOFI Database

Ichthyoplankton (fish eggs and larvae) collected by bongo and manta net tows on CalCOFI cruises, processed by SWFSC.

Ingest Underway CUFES Fish Eggs

Continuous Underway Fish Egg Sampler (CUFES) egg counts (sardine, anchovy, jack mackerel, hake, squid, other) with underway environmental conditions, from CalCOFI cruises (1996-present). Source: NOAA CoastWatch ERDDAP erdCalCOFIcufes.

Ingest SIO PIC Zooplankton Net Tows

Zooplankton net-tow sample registry from the SIO Pelagic Invertebrate Collection, filtered to the CalCOFI region. Position, time, depth, and gear metadata per tow. Biovolume measurements are not in the source file and are pending from the provider (see Questions for Data Providers).

Ingest CCE-LTER Euphausiids

Euphausiid (krill) abundance from CalCOFI / CCE-LTER net tows, 1951-2019, one row per tow. Provisional pending provider answers on abundance units and taxonomic scope (see Questions for Data Providers).

Ingest CCE-LTER ZooDB Holoplankton

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.

Ingest CCE-LTER ZooScan PRPOOS

Zooplankton abundance, carbon biomass, and size (Feret diameter, individual carbon content) from ZooScan optical imaging of CalCOFI / CCE-LTER PRPOOS net tows on lines 80, 87 and 90, 2005-present, machine-classified into 23 bioclasses (copepod groups, euphausiids, chaetognaths, appendicularians, salps, doliolids, pteropods, rhizaria and more). One row per (sample, taxon, measurement_type); per-station tows. Source: SIO Ocean Informatics ZooScan portal (Ohman Lab; interface by Marina Frants).

Publish CalCOFI tables to ERDDAP (EDDTableFromParquetFiles)

Publish Ichthyoplankton to OBIS