6  Naming conventions

These are the database’s conventions: what a table, a column, a key, a measured quantity, a life stage, a gear code, a provider or a dataset is called, and why. They are generated from the registries in CalCOFI/workflows metadata/ — the same files the ingest notebooks conform to and the release is checked against — so this chapter is the convention as enforced, not as remembered. The companion for anyone supplying data is Providing data to CalCOFI, which says which of these a provider needs to care about.

6.1 The rules

• Tables are singular and lower case: cruise, sample, taxon (not cruises).
• Columns are snake_case, lower case with underscores, so nothing ever needs quoting in SQL; a unit is a suffix where one applies (depth_m, volume_sampled_m3, temperature_degc).
• The suffix of an identifier says what it holds: *_key a string natural key, *_id an integer, *_uuid the provider’s own identifier, *_seq a sequence. The four keys that carry the integration — cruise_key, sample_key, site_key / grid_key, taxon_key — and what each promises are in Keys and integrity.
• Every measured value is a row, not a column: measurement_type, value (measurement_value on the deprecated obs), measurement_qual, with the vocabulary of types registered once (below), so a new quantity is a registry row, never a schema change.
• Text is UTF-8; a geometry column is geom, tagged EPSG:4326; times are UTC (the dictionary names an event’s start and end, datetime_start_utc / datetime_end_utc; the released sample carries the start as datetime); positions are decimal degrees, signed; depth is metres, positive down.

6.2 Fields

The field dictionary is prescriptive: a new dataset’s columns are mapped onto these names at ingest, and the aliases record what each source called them. dwc_term is the Darwin Core term a field publishes as, filled only where one term means exactly this (74 of 74 today). Table 6.1 is the dictionary itself.

Table 6.1: The field dictionary (metadata/field_dictionary.csv).

field	type	units	description	aliases	dwc
descriptive
ship_name	VARCHAR		Ship name as resolved against the NODC ship registry.	shipname;Ship_Name;ship
flag
hour_source_conflict	BOOLEAN		TRUE where two source sheets disagree on a record's start hour.
identifier
assoc_bottle_number	INTEGER		Companion bottle number for matching to CTD bottle records for other data.	Associated Bottle Number
bottle_id	INTEGER		Niskin bottle identifier; primary key of bottle.
bottle_number	INTEGER		Provider's reference number of a sample bottle on the rosette.	Bottle Number
cast_id	INTEGER		Bottle/CTD cast identifier; primary key of casts.	Cast_ID
cast_key	VARCHAR		Natural cast key.
cast_number	INTEGER		Provider's reference number for a CTD deployment within a cruise.	Cast Number
cruise_key	VARCHAR		Natural cruise key in YYYY-MM-NODC form (e.g. 1998-02-33JD); primary key of cruise.	cruise;Cruise;cruise_id;CruiseID;cruise_key_0
cruise_key_datasets	VARCHAR		Comma-separated, sorted list of dataset_key values whose sample rows carry this cruise_key -- which datasets designate or observe the cruise.
cruise_key_method	VARCHAR		Two distinct uses of one name, at two grains. (1) On a per-event staging table (casts, sample, ...): how resolve_cruise_key() settled THAT ROW's cruise_key -- span (reference cruise date span), source (the source's own YYYYMM designation), month (event month); wrangling-only, not released. (2) On the released cruise reference table itself (calcofi4db >= 3.32.0, WS-B / complete_cruise_reference()): how THAT CRUISE ROW entered the reference -- swfsc (a real SWFSC ichthyo station-occupation cruise) or derived (added at release because some other dataset designates it and the SWFSC export has no station row for it); IS released, on cruise.
cruise_uuid	UUID		Stable UUID for a cruise (SWFSC source tables).	cruise_id
grid_key	VARCHAR		CalCOFI grid-cell key, st{station}-ln{line} (_hist for a cell of the historical pattern); FK to grid. Assigned spatially via assign_grid_key(): the cell the position falls in, the key that sorts first on a shared edge.
net_uuid	UUID		Stable UUID for a plankton net sample (SWFSC source).
order_occ	SMALLINT		Order of station occupation within a cruise.	orderocc;order_occupied;Order_Occ
prev_grid_key	VARCHAR		Key of a cell of the PREVIOUS CalCOFI grid (calcofi4r::cc_grid_v1, the grid of every release through v2026.10.01); with grid_key the primary key of grid_crosswalk.
ship_code	VARCHAR		Source ship code as provided by the data provider; resolve to ship_key.	Ship_Code
ship_ices	VARCHAR		ICES platform code of the ship (SWFSC ShipLookup.ShipIces), carried beside ship_nodc on ship and cruise.	ShipIces;shipices
ship_key	VARCHAR		NODC ship code key; primary key of ship.	shipcode
ship_nodc	VARCHAR		NODC ship code.	shipnodc
site_key	VARCHAR		CalCOFI station key in 'line station' form (e.g. '090.0 062.0'); canonical spatial join key.	Sta_ID;sta_id;station_id;Station_ID;stationid	locationID
site_uuid	UUID		Stable UUID for a site occupation (SWFSC source).	stationid
source_uuid	UUID		The provider's own identifier for this event as shipped (SWFSC ichthyo site_uuid / tow_uuid / net_uuid, verbatim); NULL where the source mints none -- 15 of 16 datasets.
station_uuid	UUID		The SWFSC station-occupation UUID (= ichthyo site.source_uuid) this event belongs to: the row's own site for ichthyo itself, matched for every other dataset. See station_uuid_method for how.
station_uuid_method	VARCHAR		How station_uuid was determined: self (this row IS the ichthyo site), parent (a foreign row parented DIRECTLY to an ichthyo site, e.g. the crab's examined subsamples), order_occ (matched on cruise_key + site_key + order_occ), datetime (matched on cruise_key + site_key + a unique occupation within tolerance). NULL when station_uuid is NULL.
taxon_id	INTEGER		Dataset-local taxon key; crosswalks to the global taxon_key via dataset_taxon.
tow_id	INTEGER		Net-tow identifier (source integer counter); primary key of a tow table.	RowNumber
tow_number	INTEGER		Sequential tow number within an occupation.	townumber;tow_num
tow_uuid	UUID		Stable UUID for a net tow (SWFSC source).
measurement
avg	DOUBLE		Mean of replicate measurements at a unique position (site_key+datetime+depth+type).
measurement_type	VARCHAR		Type of measurement; FK to measurement_type. Vocabulary in metadata/measurement_type.csv.		measurementType
measurement_value	DOUBLE		Numeric value of the measurement; units carried by measurement_type, not here.		measurementValue
n_obs	INTEGER	count	Number of replicate observations aggregated.
standard_haul_factor	DOUBLE		Standard haul factor for abundance standardization.	std_haul_factor
stddev	DOUBLE		Sample standard deviation of replicates; 0 when n_obs = 1.
tally	INTEGER	count	Raw count of individuals.	Tally	organismQuantity
volume_sampled	DOUBLE	m3	Volume of water filtered/sampled.	vol_sampled_m3	sampleSizeValue
provenance
cruise_code	VARCHAR		Provider short cruise code (e.g. YYYYMM '200411'); NOT a join key.	Cruise
cruise_orig	VARCHAR		Cruise label exactly as the source provided it; cruise_key is derived from it.	Cruise;cruise_label
schema_variant	VARCHAR		Which source schema a row was read under, for datasets spanning multiple file formats.
source_row_id	INTEGER		Sequential row identifier within a single source file.	ID
station_raw	VARCHAR		Packed line/station value kept verbatim from the source, never decomposed.	Station
study_name	VARCHAR		Provider study/cruise identifier string (e.g. CCE-LTER '2004-11-02-C-33RR').	studyName
quality
measurement_qual	VARCHAR		Quality flag or comment for the measurement.
spatial
bottom_depth_m	DOUBLE	m	Seafloor (bottom) depth, in meters.	Bottom_D
depth_m	DOUBLE	m	Sampling depth below surface, in meters.	Depthm;depth;Depth
geom	GEOMETRY		Feature geometry in WGS84 (EPSG:4326).		footprintWKT
grid_frac	DOUBLE		overlap_km2 as a fraction of the CURRENT cell's whole area. Sums over a current cell to one, less the part no previous cell covered; slightly over one where previous cells overlap each other (line 93.3 / line 100).
hex7	UBIGINT		H3 cell at resolution 7 that is the PARENT of the resolution-10 cell (hex_id) of the row's own position; NULL where the position is missing or not finite. Not the resolution-7 cell the position falls in: H3 cells do not nest exactly, and the two differ near every cell edge. One definition on every table that carries it, so an observation and a sampling event at the same position share a hexagon.
hex_id	UBIGINT		H3 cell of the row's position at resolution 10 (calcofi4db CC_H3_RES_MAX), as an unsigned 64-bit integer; NULL where the position is missing or not finite. Coarser hexagons are h3_cell_to_parent(hex_id, res), or calcofi4db::h3_parent_sql() without the h3 extension.
latitude	DOUBLE	decimal_degrees	Latitude in decimal degrees, WGS84 (EPSG:4326).	lat_dec;Lat_Dec;latidude;lat	decimalLatitude
line	DOUBLE		Alongshore component of the CalCOFI coordinate system (https://proj.org/en/stable/operations/projections/calcofi.html).	Line
longitude	DOUBLE	decimal_degrees	Longitude in decimal degrees, WGS84 (EPSG:4326).	lon_dec;Lon_Dec;lon	decimalLongitude
overlap_km2	DOUBLE	km2	Area the previous cell (prev_grid_key) and the current cell (grid_key) share, in California Albers (EPSG:3310), rounded to the square metre.
prev_frac	DOUBLE		overlap_km2 as a fraction of the PREVIOUS cell's whole area: the weight that carries a value keyed on the previous grid to the current cells. Sums over a previous cell to one, less the part of it no current cell covers (land under the finer coastline); never rescaled.
seafloor_depth_m	DOUBLE	m	Seafloor depth at the sample position from GEBCO 2025 (bilinear; positive down; 0 on land; NULL outside the raster). Stamped on sample at release by calcofi4db::add_sample_seafloor(); compare with depth_max_m, allowing for the ~460 m GEBCO cell and minute-rounded historical positions.
station	DOUBLE		Offshore component of the CalCOFI coordinate system (https://proj.org/en/stable/operations/projections/calcofi.html).	Station
taxonomic
common_name	VARCHAR		Common (vernacular) name of the taxon.		vernacularName
itis_id	INTEGER		ITIS Taxonomic Serial Number (TSN) for the taxon.	tsn;itis_tsn;TSN
life_stage	VARCHAR		Life stage of the organism (e.g. egg, yolk-sac larva).	stage	lifeStage
scientific_name	VARCHAR		Scientific (Latin) name of the taxon.	taxon;Taxon	scientificName
species_id	SMALLINT		CalCOFI species identifier; primary key of species.	sppcode;SppCode;calcofi_species_code
worms_id	INTEGER		WoRMS AphiaID for the taxon.	aphiaid;AphiaID
temporal
cruise_month	TINYINT		The observation's cruise's month (cruise.month_median; the cruise_key's MM where the cruise table lacks it), the month its anomaly is matched to the climatology on.
date_max	DATE		Last event date observed for a cruise (from its own tows).
date_median	DATE		The median datetime (UTC) of a cruise's root samples (casts, station occupations, bottle casts); its calendar month is the cruise's month, which every anomaly and season filter keys on. NULL for a cruise with no dated sample.
date_min	DATE		First event date observed for a cruise (from its own tows); with date_max the span calcofi4db::resolve_cruise_key() matches events against.
date_ym	DATE		Year-month of the cruise (first day of month).	cruise_ymd
datetime_end_utc	TIMESTAMP		Sampling-event end date-time in UTC (datetime_start_utc holds the start); e.g. net-tow end.	time_end;TowEnd
datetime_start_utc	TIMESTAMP		Observation (or sampling-event start) date-time in UTC. For instantaneous samples this is the sample time; for tows/casts it is the start.	datetime_utc;time_start;starttime;date_time_utc;datetime;TowBegin	eventDate
month_median	TINYINT		The cruise's month: the month of date_median, else the MM of its cruise_key. A cruise ID names sometimes the month a cruise started and sometimes the month it mostly covered, so the median cast date is the month the cruise samples (Rasmus Swalethorp 2026-10-16, Ben Best 2026-10-20).
quarter	TINYINT		The cruise's season as a number, 1 = DJF, 2 = MAM, 3 = JJA, 4 = SON, from the cruise's month (calcofi4db::cruise_quarter_sql(), 4.34.0; Q1 Jan-Mar ... Q4 Oct-Dec through release v2026.10.30). The Explorer's season filter and the climatology's seasonal baseline (season_*) key on it.
season	VARCHAR		The cruise's meteorological season from month_median: DJF (winter), MAM (spring), JJA (summer), SON (fall) — calcofi4db::cruise_season_sql(). The numeric twin is quarter (1 = DJF ... 4 = SON).
season_year	SMALLINT		The year the cruise's season belongs to: the year of date_median (else of the key), plus one for December, so December counts toward the following year's winter (Dec 2025 + Jan-Feb 2026 = winter 2026) and a winter is never split across two years.

6.3 Measured quantities

measurement_type.csv is the vocabulary of everything measured, filed under the twelve categories every dataset and type belongs to. A type carries its units, the physical bounds a value must lie within (valid_min / valid_max — enforced per dataset at ingest, and a release fails on a value outside them), the depth range over which it is defined, how a derived type was produced, and — where one concept says exactly this — the NERC P01 concept and P06 unit a Darwin Core export emits. is_canonical marks the headline types the apps offer first. The categories are Table 6.2, the types themselves Table 6.3.

Table 6.2: The twelve categories (metadata/category.csv).

category	realm	description	measurement types	datasets
Physical Oceanography	env	Temperature, salinity, density, oxygen, pressure and dynamic height from bottles and CTD casts	104	4
Nutrients & Chemistry	env	Nitrate, nitrite, phosphate, silicate and ammonium from bottle samples; particulate and total organic carbon and nitrogen, nitrate isotopes, and trace metals (iron)	19	1
Carbonate System	env	Dissolved inorganic carbon, alkalinity, pH and pCO2	15	1
Productivity & Pigments	env	Chlorophyll a, phaeopigments, primary production (C14) and light (PAR)	67	0
Meteorology & Sea State	env	Wind, air temperature, pressure, cloud, visibility, sea state and water colour from the underway METS and ship observations	21	1
Phytoplankton	bio	Phytoplankton counts by taxon or functional group, and imaging flow cytometry (IFCB)	5	1
Picoplankton & Bacteria	bio	Picoplankton and bacterioplankton abundances by flow cytometry	5	1
Zooplankton	bio	Net-tow zooplankton: displacement volume, imaged and identified taxa, decapod larvae	21	5
Euphausiids (Krill)	bio	Euphausiid species and stages from bongo tows	1	1
Fish Eggs & Larvae	bio	Ichthyoplankton — fish eggs and larvae from oblique and vertical tows and the continuous underway egg sampler	15	2
Mesopelagic Fish	bio	Midwater trawl catches of mesopelagic fishes	0	1
Seabirds & Marine Mammals	bio	Strip-transect counts of seabirds and marine mammals along the cruise track	13	1
Genomics & eDNA	bio	Metabarcoding and environmental DNA — ASV tables, eDNA-derived abundance and density	10	1

Table 6.3: Every measurement type (298), by category. Bounds are physical limits, not observed ranges; a blank NERC column means no concept states exactly this, never that it was not looked at.

measurement type	canonical	units	bounds	description	P01
Carbonate System
alkalinity	yes	umol/kg	0 – 5000	Total alkalinity	MDMAP014
alkalinity_rep1	yes	umol/kg	0 – 5000	Total alkalinity replicate 1	MDMAP014
alkalinity_rep2	yes	umol/kg		Total alkalinity replicate 2	MDMAP014
dic	yes	umol/kg	0 – 5000	Dissolved inorganic carbon	TCO2MSXX
dic_rep1	yes	umol/kg	0 – 5000	Dissolved inorganic carbon replicate 1	TCO2MSXX
dic_rep2	yes	umol/kg		Dissolved inorganic carbon replicate 2	TCO2MSXX
ph	yes	pH	6 – 9	pH	PHXXZZXX
ph_rep1	yes	pH		pH replicate 1	PHXXZZXX
ph_rep2	yes	pH		pH replicate 2	PHXXZZXX
sw_ph	yes		6 – 9	Seawater pH
dic_pco2_raw				Underway DIC raw pCO2
dic_ph_raw				Underway DIC raw pH
dic_salinity_psu		PSU		Underway DIC system salinity
dic_temp_c		deg_C		Underway DIC system temperature
dic_valve				Underway DIC valve state
Euphausiids (Krill)
euphausiid_abundance	yes	numberPerMeterSquared	≥ 0	Euphausiid (krill) abundance per net tow, by species and life stage; vertically integrated individuals beneath 1 m2 of sea surface (EDI knb-lter-cce.313.1).
Fish Eggs & Larvae
abundance	yes	count	≥ 0	Specimen count per net tow (headline occurrence; standardize via std_haul_factor)
body_length	yes	mm		Larva body length (obs_freq binned attribute)	OBSINDLX
egg_concentration	yes	count/m3	≥ 0	Fish or squid eggs per cubic metre of water pumped by the Continuous Underway Fish Egg Sampler (CUFES): the sample's egg count standardized by its minutes sampled and its mean pump speed
prop_sorted	yes	dimensionless		Fraction of the sample sorted (event-level effort)
small_plankton_biomass	yes	mL		Small plankton displacement-volume biomass (event-level)
stage	yes			Egg or larva developmental stage (obs_freq binned attribute; labeled via lookup)
std_haul_factor	yes	dimensionless		Standardized haul factor (Smith & Richardson 1977; event-level effort)
total_plankton_biomass	yes	mL		Total plankton displacement-volume biomass (event-level)
volume_sampled	yes	m3		Volume of water filtered by the net (event-level effort)
anchovy_eggs		count		Northern anchovy egg count
hake_eggs		count		Pacific hake egg count
jack_mackerel_eggs		count		Jack mackerel egg count
other_fish_eggs		count		Other fish egg count
sardine_eggs		count		Sardine egg count
squid_eggs		count		Squid egg count
Genomics & eDNA
dna_concentration	yes	ng/uL	≥ 0	Concentration of total DNA after extraction from an eDNA filter
edna_asvs_12s	yes	count	≥ 0	Distinct amplicon sequence variants (ASVs) assigned to taxa by the 12S rRNA MiFish assay, per sample, over its PCR replicate libraries
edna_asvs_dloop	yes	count	≥ 0	Distinct amplicon sequence variants (ASVs) assigned to taxa by the mitochondrial D-loop assay, per sample, over its PCR replicate libraries
edna_presence	yes	dimensionless	0 – 1	Detection (1) or non-detection (0) of the taxon in a sequenced seawater eDNA sample; 0 is not a confirmed absence, and a sample that failed PCR publishes no value (headline occurrence). For calcofi_2022-edna only detections (1) are emitted, so the absence of a row is not a non-detection there; sio_cetacean-edna emits 0 for a sequenced sample with no detection
edna_reads_12s	yes	reads	≥ 0	DNA sequence reads assigned to the taxon by the 12S rRNA MiFish metabarcoding assay (fish), per sample; semi-quantitative, not abundance
edna_reads_dloop	yes	reads	≥ 0	DNA sequence reads assigned to the taxon by the mitochondrial D-loop metabarcoding assay (cetaceans), per sample; semi-quantitative, not abundance
edna_reads_filtered_12s	yes	reads	≥ 0	Sequence reads retained after bioinformatic filtering by the 12S MiFish assay, per sample (normaliser for edna_reads_12s)
edna_reads_filtered_dloop	yes	reads	≥ 0	Sequence reads retained after bioinformatic filtering by the D-loop assay, per sample (normaliser for edna_reads_dloop)
edna_reads_raw_12s	yes	reads	≥ 0	Raw sequence reads produced by the 12S MiFish assay before bioinformatic filtering, per sample
edna_reads_raw_dloop	yes	reads	≥ 0	Raw sequence reads produced by the D-loop assay before bioinformatic filtering, per sample
Meteorology & Sea State
air_temp_c	yes	deg_C	-50 – 60	Air temperature
atm_pressure_mb	yes	mb	800 – 1100	Atmospheric pressure (ship level)
barometric_pressure	yes	millibars		Barometric pressure	CAPHZZ01
beaufort	yes	Beaufort	0 – 12	Beaufort sea state at a cetacean sighting (obs_attribute, bin_value)
cloud_amount	yes	oktas		Cloud amount in oktas (WMO 2700)	WMOCCCAC
cloud_type	yes			WMO cloud type code (WMO 0500)	WMOCCTAC
long_wave_rad	yes	W/m2		Longwave radiation
rel_humidity_pct	yes	percent		Relative humidity
secchi_depth	yes	meters		Secchi disk depth	SECCSDNX
short_wave_rad	yes	W/m2		Shortwave radiation
visibility	yes			WMO visibility code (WMO 4300)	WMOCHVXX
water_color	yes	Forel-Ule		Water color on Forel-Ule scale	CLFORULE
wave_direction	yes	degrees		Wave direction (abbreviated 360 degree azimuth)	WMOCWDXX
wave_height	yes	feet		Wave height
wave_period	yes	seconds		Wave period
weather_code	yes			WMO weather code (WMO 4501)	WMOCPWXX
wind_dir_deg	yes	degrees	0 – 360	Wind direction
wind_direction	yes	degrees		Wind direction (abbreviated 360 degree azimuth)	EWDAZZ01
wind_speed	yes	knots		Wind speed	EWSBZZ01
wind_speed_ms	yes	m/s	0 – 120	Wind speed
atm_pressure_slc_mb		mb		Atmospheric pressure (sea-level corrected)
Nutrients & Chemistry
ammonia	yes	umol/L	0 – 100	Ammonium concentration (QC'd; the source column is named NH3)	AMONZZXX
btl_ammonium	yes	umol/L	0 – 100	Bottle ammonium	AMONZZXX
btl_nitrate	yes	umol/L	0 – 100	Bottle nitrate	NTRAZZXX
btl_nitrite	yes	umol/L	0 – 10	Bottle nitrite	NTRIZZXX
btl_phosphate	yes	umol/L	0 – 10	Bottle phosphate	PHOSZZXX
btl_silicate	yes	umol/L	0 – 300	Bottle silicate	SLCAZZXX
dissolved_iron	yes	nmol/L	≥ 0	Dissolved iron (Fe) concentration
est_nitrate_cruise_corr	yes	umol/L	0 – 200	Est. nitrate cruise-corrected
est_nitrate_sta_corr	yes	umol/L	0 – 200	Est. nitrate station-corrected
isus_v	yes	V	-1 – 10	ISUS nitrate voltage
nitracline_depth	yes	m	0 – 6500	Nitracline depth: where nitrate reaches 1 umol/L, interpolated between the bracketing samples
nitrate	yes	umol/L	-1 – 60	Nitrate concentration	NTRAZZXX
nitrite	yes	umol/L	0 – 10	Nitrite concentration	NTRIZZXX
phosphate	yes	umol/L	0 – 10	Phosphate concentration	PHOSZZXX
poc	yes	umol/L	≥ 0	Particulate organic carbon (POC)
pon	yes	umol/L	≥ 0	Particulate organic nitrogen (PON)
silicate	yes	umol/L	0 – 300	Silicate concentration	SLCAZZXX
toc	yes	umol/L	≥ 0	Total organic carbon (TOC: dissolved plus particulate organic carbon)
r_ammonium		umol/L	0 – 100	Reported ammonium concentration (pre-QC)	AMONZZXX
Physical Oceanography
beam_attenuation	yes	1/m		Beam attenuation coefficient	ATTNXXZZ
bottom_depth_m	yes	m	0 – 11000	Bottom depth (single-beam)
btl_depth	yes	m	0 – 11000	Bottle trip depth	ADEPZZ01
btl_temperature	yes	degC	-2 – 40	Bottle temperature	TEMPPR01
buoyancy_n2	yes	1/s2	-0.2 – 0.2	Buoyancy (Brunt-Vaisala) frequency squared N2 (TEOS-10), 10 m running mean
buoyancy_n2_max	yes	1/s2	-0.2 – 0.2	Maximum buoyancy frequency squared N2 (TEOS-10, 10 m running mean) between 10 and 200 m, at pycnocline_depth
ctdtemp_its90	yes	degC	-2 – 40	CTD temperature (ITS-90 scale)	TEMPST01
dry_air_temp	yes	degC		Dry air temperature from sling psychrometer	CDTASS01
dynamic_height	yes	dyn m	-50 – 50	Dynamic height
hypoxic_depth_05	yes	m	0 – 6500	Severe hypoxic boundary depth (core of the oxygen minimum zone): the shallowest depth where oxygen falls to 0.5 mL/L
hypoxic_depth_14	yes	m	0 – 6500	Hypoxic boundary depth: the shallowest depth where oxygen falls to 1.4 mL/L
hypoxic_depth_24	yes	m	0 – 6500	Mild hypoxic boundary depth: the shallowest depth where oxygen falls to 2.4 mL/L
mld_sigma_theta_002	yes	m	0 – 6500	Mixed-layer depth: where sigma-theta is 0.02 kg/m3 greater than at 10 m (CalCOFI legacy definition)
mld_sigma_theta_0125	yes	m	0 – 6500	Mixed-layer depth, sigma-theta increase of 0.125 kg/m3 from 10 m (Levitus 1982)
mld_temperature_02	yes	m	0 – 6500	Mixed-layer depth, temperature departure of 0.2 degC from 10 m (de Boyer Montegut et al. 2004)
oxygen	yes		0 – 20	Dissolved oxygen
oxygen_btl_ml_l	yes	ml/L	0 – 15	Bottle dissolved oxygen	DOXYZZXX
oxygen_btl_umol_kg	yes	umol/kg	0 – 700	Bottle dissolved oxygen	DOXMZZXX
oxygen_mg_l	yes	mg/L	0 – 20	Dissolved oxygen in mg/L (the unit an eDNA filter's co-collected chemistry reports; see oxygen_btl_ml_l / oxygen_umol_kg for the other oxygen units)
oxygen_ml_l	yes	ml/L	-0.5 – 15	Dissolved oxygen (QC'd)	DOXYZZXX
oxygen_ml_l_1	yes	ml/L	0 – 15	DO sensor 1 (uncorrected)	DOXYZZXX
oxygen_ml_l_1_cruise_corr	yes	ml/L	0 – 15	DO sensor 1 cruise-corrected	DOXYZZXX
oxygen_ml_l_1_sta_corr	yes	ml/L	0 – 15	DO sensor 1 station-corrected	DOXYZZXX
oxygen_ml_l_2	yes	ml/L	0 – 15	DO sensor 2 (uncorrected)	DOXYZZXX
oxygen_ml_l_2_cruise_corr	yes	ml/L	0 – 15	DO sensor 2 cruise-corrected	DOXYZZXX
oxygen_ml_l_2_sta_corr	yes	ml/L	0 – 15	DO sensor 2 station-corrected	DOXYZZXX
oxygen_ml_l_ave_cruise_corr	yes	ml/L	0 – 15	DO average cruise-corrected	DOXYZZXX
oxygen_ml_l_ave_sta_corr	yes	ml/L	0 – 15	DO average station-corrected	DOXYZZXX
oxygen_saturation	yes	%	-1 – 250	Oxygen percent saturation	OXYSZZ01
oxygen_umol_kg	yes	umol/kg	-20 – 700	Dissolved oxygen (QC'd)	DOXMZZXX
oxygen_umol_kg_1	yes	umol/kg	0 – 700	DO sensor 1 (uncorrected)	DOXMZZXX
oxygen_umol_kg_2	yes	umol/kg	0 – 700	DO sensor 2 (uncorrected)	DOXMZZXX
oxygen_umol_kg_ave_sta_corr	yes	umol/kg	0 – 700	DO average station-corrected	DOXMZZXX
pressure	yes	dbar	0 – 6500	Pressure	PRESPR01
pycnocline_depth	yes	m	10 – 200	Pycnocline depth: where the buoyancy frequency squared N2 (TEOS-10, 10 m running mean) is greatest between 10 and 200 m
salinity	yes	PSS-78	0 – 45	Salinity - Practical Salinity Scale 1978 (QC'd)	PSLTZZ01
salinity_1	yes	PSU	0 – 45	Salinity sensor 1 (uncorrected)	PSALST01
salinity_1_corr	yes	PSU	0 – 45	Salinity sensor 1 cruise-corrected	PSALST01
salinity_2	yes	PSU	0 – 45	Salinity sensor 2 (uncorrected)	PSALST02
salinity_2_corr	yes	PSU	0 – 45	Salinity sensor 2 cruise-corrected	PSALST02
salinity_ave_corr	yes	PSU	0 – 45	Average salinity corrected	PSLTZZ01
salinity_btl	yes	PSU	0 – 45	Bottle salinity	PSLTZZ01
salinity_pss78	yes	PSS-78	0 – 45	Practical salinity (PSS-78)	PSLTZZ01
sigma_theta	yes	kg/m3	15 – 35	Potential density (Sigma Theta), legacy DECODR value	SIGTEQ01
sigma_theta_1	yes	kg/m3	15 – 35	Potential density sensor 1	SIGTPR01
sigma_theta_ave	yes	kg/m3	15 – 35	Potential density anomaly (sigma-theta), sensor-pair average by the provider's flags
sigma_theta_teos10	yes	kg/m3	-8 – 37	Potential density anomaly (sigma-theta, TEOS-10) per bottle, from the bottle's own temperature and salinity	SIGTPR03
specific_volume_anomaly	yes	10^-8 m3/kg		Specific volume anomaly
spiciness0	yes	kg/m3	-25 – 18	Spice (spiciness at 0 dbar, TEOS-10); positive spicy (warm, salty), negative minty
sss_psu	yes	PSU	0 – 45	Sea surface salinity (raw)
sst_c	yes	deg_C	-2 – 40	Sea surface temperature (raw)
temperature	yes	degC	-2 – 40	Water temperature (QC'd)	TEMPPR01
temperature_ave	yes	degC	-2 – 40	Average temperature	TEMPPR01
transmissometer	yes	%		Light transmissometer
tsg1_salinity_psu	yes	PSU	0 – 45	TSG unit 1 salinity
tsg1_temp_c	yes	deg_C	-2 – 40	TSG unit 1 temperature (physical sensor unconfirmed -- mets_03)
uws_flow	yes	L/min	≥ 0	Underway seawater flow rate
wet_air_temp	yes	degC		Wet air temperature from sling psychrometer	CWETSS01
bottom_depth		m		Water depth at the sampling event (sea floor depth beneath the cast)
bottom_depth_mb_m		m		Bottom depth (multibeam)
mld_sigma_theta_003		m	0 – 6500	RETIRED: mixed-layer depth, sigma-theta increase of 0.03 kg/m3 from 10 m (de Boyer Montegut et al. 2004)
oxygen_sat_pct		percent	0 – 200	Dissolved oxygen saturation
oxygen_saturation_1		%		Oxygen saturation sensor 1	OXYSZZ01
oxygen_saturation_2		%		Oxygen saturation sensor 2	OXYSZZ01
oxygen_temp_c		deg_C		Oxygen sensor temperature
oxygen_umol_kg_1_cruise_corr		umol/kg	0 – 700	DO sensor 1 cruise-corrected	DOXMZZXX
oxygen_umol_kg_1_sta_corr		umol/kg	0 – 700	DO sensor 1 station-corrected	DOXMZZXX
oxygen_umol_kg_2_cruise_corr		umol/kg	0 – 700	DO sensor 2 cruise-corrected	DOXMZZXX
oxygen_umol_kg_2_sta_corr		umol/kg	0 – 700	DO sensor 2 station-corrected	DOXMZZXX
potential_temperature_1		degC	-2 – 40	Potential temperature sensor 1
potential_temperature_2		degC	-2 – 40	Potential temperature sensor 2
pred_sal_psu			0 – 45	Model-predicted salinity
pred_sst_c				Model-predicted sea-surface temperature (distinct from Pred_TSGTemp)
pred_temp_c				Model-predicted temperature
r_depth		m	0 – 11000	Reported depth from pressure (pre-QC)	ADEPZZ01
r_dynamic_height		dyn m	-10 – 10	Reported dynamic height, legacy DECODR value (no QC'd counterpart)
r_oxygen_umol_kg		umol/kg		Reported oxygen (pre-QC)	DOXMZZXX
r_salinity_sva		10^-8 m3/kg		Reported Specific Volume Anomaly (pre-QC); WARNING: different parameter/scale than salinity PSS-78
r_temperature		degC		Reported potential temperature (pre-QC)
sigma_theta_2		kg/m3	15 – 35	Potential density sensor 2	SIGTPR02
ss_conductivity		S/m	0 – 10	Sea surface conductivity (independent sensor)
sss_psu_corrected		PSU	0 – 45	Corrected sea surface salinity
sst_c_corrected		deg_C		Corrected sea surface temperature
temperature_1		degC	-2 – 40	Temperature sensor 1	TEMPST01
temperature_2		degC	-2 – 40	Temperature sensor 2	TEMPST02
transmissometer_v		V	-1 – 15	Transmissometer voltage
tsg1_conductivity		S/m		TSG unit 1 conductivity
tsg1_density		kg/m3		TSG unit 1 density
tsg1_salinity_psu_calibrated		PSU	0 – 45	Calibrated salinity
tsg1_sound_velocity		m/s		TSG unit 1 sound velocity
tsg1_temp_c_calibrated		deg_C	-2 – 40	Calibrated temperature
tsg2_conductivity		S/m	0 – 10	TSG unit 2 conductivity
tsg2_density		kg/m3		TSG unit 2 density
tsg2_salinity_psu		PSU		TSG unit 2 salinity
tsg2_sound_velocity		m/s		TSG unit 2 sound velocity
tsg2_temp_c		deg_C		TSG unit 2 temperature (physical sensor unconfirmed -- mets_03)
tsg2b_temp_c		deg_C	-2 – 40	A SECOND unit-2 temperature appearing alongside TSG_Temp_2 in one file
tsg3_conductivity		S/m		TSG unit 3 conductivity
tsg3_density		kg/m3	900 – 1100	TSG unit 3 density
tsg3_salinity_psu		PSU	0 – 45	TSG unit 3 salinity
tsg3_sound_velocity		m/s		TSG unit 3 sound velocity
tsg3_temp_c		deg_C	-2 – 40	TSG unit 3 temperature (physical sensor unconfirmed -- mets_03)
tsg5_salinity_psu		PSU	0 – 45	TSG unit 5 salinity
tsg5_temp_c		deg_C	-2 – 40	TSG unit 5 temperature (physical sensor unconfirmed -- mets_03)
Phytoplankton
ifcb_abundance	yes	number/ml	0 – 1e+05	Phytoplankton abundance by imaging flow cytometry (IFCB): images (cells) per ml of seawater analysed, per taxon; the taxon is obs.taxon_key
ifcb_biovolume	yes	um3/ml	0 – 1e+09	Phytoplankton biovolume concentration by imaging flow cytometry (IFCB): total cell biovolume per ml of seawater analysed, per taxon
ifcb_size_class	yes	count	≥ 0	Equivalent-spherical-diameter (ESD) size class of the imaged cells of a taxon in an IFCB sample (obs_attribute): bin_label is the class, count the images in it
ifcb_volume_analyzed	yes	ml	0 – 25	Volume of seawater analysed by the IFCB for a sample (the denominator of ifcb_abundance)
phytoplankton_abundance		cells/L		Phytoplankton abundance by inverted-microscope count (cells/L)
Picoplankton & Bacteria
het_bacteria	yes	number/ml	≥ 0	Heterotrophic bacteria abundance (FCM)
picoeukaryotes	yes	number/ml	≥ 0	Picoeukaryote abundance (FCM)
picoplankton_abundance	yes	number/ml	≥ 0	Picoplankton and bacteria cell abundance by flow cytometry (FCM); the population counted is obs.taxon_key
prochlorococcus	yes	number/ml	≥ 0	Prochlorococcus abundance (FCM); ~80% populated, see Q01	P701A90Z
synechococcus	yes	number/ml	≥ 0	Synechococcus abundance (FCM)	P700A90Z
Productivity & Pigments
btl_chlorophyll_a	yes	ug/L	-1 – 100	Bottle chlorophyll-a	CPHLZZXX
btl_phaeopigment	yes	ug/L	-5 – 100	Bottle phaeopigment	PHAEZZXX
c14_dark	yes	mgC/m3/hld		14C assimilation dark/control bottle
c14_mean	yes	mgC/m3/hld		Mean 14C assimilation of replicates 1 and 2
c14_rep1	yes	mgC/m3/hld		14C assimilation replicate 1
c14_rep2	yes	mgC/m3/hld		14C assimilation replicate 2
chl_a_gt8um_int_100m	yes	mg/m2	≥ 0	Chlorophyll-a retained on an 8 um membrane filter, integrated 0-100 m: one physically integrated sample combined from the ten shallowest bottles (MLRG size fractionation, 1994-1996)
chl_a_int_100m	yes	mg/m2	≥ 0	Total chlorophyll-a (GF/F filters, fluorometric) from the ten shallowest bottles, integrated algebraically 0-100 m (MLRG size fractionation, 1994-1996)
chl_fluor	yes	ug/L	≥ -1	Fluorescence (calibrated)
chl_integrated	yes	mg/m2	0 – 2e+05	Chlorophyll-a integrated over the top 200 m (or the cast bottom): the sum of the 1 m bins
chl_integrated_depth	yes	m	0 – 200	Depth reached by chl_integrated (200 m unless the cast is shallower)
chl_max	yes	ug/L	0 – 1000	Chlorophyll-a at its maximum: the 3 m running mean at chl_max_depth
chl_max_depth	yes	m	0 – 200	Depth of the chlorophyll-a maximum (DCM): the highest value of a 3 m running mean
chlorophyll_a	yes	ug/L	≥ -1	Chlorophyll-a measured fluorometrically	CPHLZZXX
est_chlorophyll_a_cruise_corr	yes	ug/L	0 – 1000	Est. chlorophyll-a cruise-corrected
est_chlorophyll_a_sta_corr	yes	ug/L	0 – 1000	Est. chlorophyll-a station-corrected
fluorescence_v	yes	V	-1 – 15	Fluorescence voltage
hplc_allo_sio	yes	ug/L	≥ 0	Alloxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_allo_umces	yes	ug/L	≥ 0	Alloxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_but_fuco_sio	yes	ug/L	≥ 0	19'-butanoyloxyfucoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_but_fuco_umces	yes	ug/L	≥ 0	19'-butanoyloxyfucoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_carotene_sio	yes	ug/L	≥ 0	Carotene by HPLC, Goericke Lab, SIO (2002-2014)
hplc_carotene_umces	yes	ug/L	≥ 0	Carotene by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_chl_a_sio	yes	ug/L	≥ 0	Chlorophyll a (monovinyl) by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chl_a_umces	yes	ug/L	≥ 0	Chlorophyll a (monovinyl) by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_chl_b_sio	yes	ug/L	≥ 0	Chlorophyll b by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chl_b_umces	yes	ug/L	≥ 0	Chlorophyll b by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_chl_c12_umces	yes	ug/L	≥ 0	Chlorophyll c1 + c2 by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_chl_c1_sio	yes	ug/L	≥ 0	Chlorophyll c1 by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chl_c2_sio	yes	ug/L	≥ 0	Chlorophyll c2 by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chl_c3_sio	yes	ug/L	≥ 0	Chlorophyll c3 by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chl_c3_umces	yes	ug/L	≥ 0	Chlorophyll c3 by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_chl_c_sio	yes	ug/L	≥ 0	Chlorophyll c (reported without a c1/c2 split) by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chlide_a_sio	yes	ug/L	≥ 0	Chlorophyllide a by HPLC, Goericke Lab, SIO (2002-2014)
hplc_chlide_a_umces	yes	ug/L	≥ 0	Chlorophyllide a by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_diadino_sio	yes	ug/L	≥ 0	Diadinoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_diadino_umces	yes	ug/L	≥ 0	Diadinoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_diato_sio	yes	ug/L	≥ 0	Diatoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_diato_umces	yes	ug/L	≥ 0	Diatoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_dvchl_a_sio	yes	ug/L	≥ 0	Divinyl chlorophyll a by HPLC, Goericke Lab, SIO (2002-2014)
hplc_dvchl_a_umces	yes	ug/L	≥ 0	Divinyl chlorophyll a by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_dvchl_b_umces	yes	ug/L	≥ 0	Divinyl chlorophyll b by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_fuco_sio	yes	ug/L	≥ 0	Fucoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_fuco_umces	yes	ug/L	≥ 0	Fucoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_hex_fuco_sio	yes	ug/L	≥ 0	19'-hexanoyloxyfucoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_hex_fuco_umces	yes	ug/L	≥ 0	19'-hexanoyloxyfucoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_lutein_umces	yes	ug/L	≥ 0	Lutein by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_neo_sio	yes	ug/L	≥ 0	Neoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_neo_umces	yes	ug/L	≥ 0	Neoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_peridinin_sio	yes	ug/L	≥ 0	Peridinin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_peridinin_umces	yes	ug/L	≥ 0	Peridinin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_phide_a_umces	yes	ug/L	≥ 0	Phaeophorbide a by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_phytin_a_umces	yes	ug/L	≥ 0	Pheophytin a by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_prasino_sio	yes	ug/L	≥ 0	Prasinoxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_prasino_umces	yes	ug/L	≥ 0	Prasinoxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_tchl_a_sio	yes	ug/L	≥ 0	Total chlorophyll a (TChl a = Chl a + DVChl a + Chlide a) by HPLC, Goericke Lab, SIO (2002-2014)
hplc_tchl_a_umces	yes	ug/L	≥ 0	Total chlorophyll a (TChl a = Chl a + DVChl a + Chlide a) by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_viola_sio	yes	ug/L	≥ 0	Violaxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_viola_umces	yes	ug/L	≥ 0	Violaxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
hplc_zea_sio	yes	ug/L	≥ 0	Zeaxanthin by HPLC, Goericke Lab, SIO (2002-2014)
hplc_zea_umces	yes	ug/L	≥ 0	Zeaxanthin by HPLC, Horn Point Laboratory, UMCES (2014-2023)
light_pct	yes	%	0 – 100	Light intensity of incubation tubes
par	yes	uE/m2/s	-100 – 5000	Photosynthetically active radiation
par_surf	yes			Surface photosynthetically active radiation
phaeopigment	yes	ug/L	≥ -5	Phaeopigment measured fluorometrically	PHAEZZXX
spar	yes	uE/m2/s	-100 – 5000	Surface PAR
pred_chl		ug/L		Estimated chlorophyll-a
Seabirds & Marine Mammals
acoustic_presence	yes	dimensionless	0 – 1	Presence (1) or absence (0) of the taxon's calls in one hour of sonobuoy recording, scanned as 60-s spectrogram windows (headline occurrence; the call types heard are obs_attribute call_type)
behavior	yes			Seabird/marine-mammal behavior category (obs_attribute; e.g. Flying, Feeding)
calf_count	yes	count	≥ 0	Number of calves in a sighted cetacean group (obs_attribute)
call_type	yes			Marine mammal call type heard in an hour of sonobuoy recording (obs_attribute; e.g. blue whale B call, fin whale 20 Hz song)
count	yes	count	≥ 0	Organism count per survey transect
effort_status	yes		0 – 1	Whether a cetacean sighting was made on effort and on transect (bin_label ON, bin_value 1) or not (OFF, 0), the analyst-adjusted flag (obs_attribute). A sampling regime, not a quality flag: line-transect density uses ON only.
group_size	yes	count	≥ 0	Best estimate of the number of individuals in a sighted cetacean group, visual line-transect survey (headline occurrence per sighting)
group_size_max	yes	count	≥ 0	Observers' maximum estimate of group size for a cetacean sighting (obs_attribute)
group_size_min	yes	count	≥ 0	Observers' minimum estimate of group size for a cetacean sighting (obs_attribute)
perp_distance	yes	m	0 – 15000	Perpendicular distance from the ship's trackline to a sighted cetacean group (obs_attribute, bin_value): the radial distance x |sin(angle off the bow)|, the lab's own value except where it was computed from the horizon distance
radial_distance	yes	m	0 – 15000	Radial (line-of-sight) distance from the ship to a sighted cetacean group (obs_attribute, bin_value): from the binocular reticle reading and the observer's eye height, or the recorded distance, whichever reproduces the lab's perpendicular distance
sighting_angle	yes	degree	0 – 180	Angle between the ship's heading and the line of sight to a sighted cetacean group, 0 dead ahead to 180 astern (obs_attribute, bin_value), with the side in bin_label (port / starboard)
transect_length	yes	km	≥ 0	Length of an on-effort, on-transect visual survey segment (event-level effort)
Zooplankton
carapace_length	yes	mm	0 – 100	Carapace length of an individual crab larva (rostrum tip to posterior margin of carapace)	CAPLEN01
settled_volume_ml	yes	ml	0 – 10000	Settled volume of the preserved plankton sample (event-level context)
zooplankton_abundance	yes	count/1000m3	≥ 0	Zooplankton numerical abundance (volumetric density) per net tow, by higher taxon. Raw (uncorrected for net type).
zooplankton_biomass_carbon	yes	mgC/m2	≥ 0	Zooplankton carbon biomass per net tow, by higher taxon. Raw (uncorrected for net type).
zooscan_abundance	yes	count/m2	≥ 0	Zooplankton areal abundance from ZooScan optical imaging, by image-classified bioclass.
zooscan_biomass_carbon	yes	mgC/m2	≥ 0	Estimated zooplankton carbon biomass from ZooScan optical imaging, by bioclass.
phyllosoma_stage_1		count		Phyllosoma stage 1 count
phyllosoma_stage_10		count		Phyllosoma stage 10 count
phyllosoma_stage_11		count		Phyllosoma stage 11 count
phyllosoma_stage_2		count		Phyllosoma stage 2 count
phyllosoma_stage_3		count		Phyllosoma stage 3 count
phyllosoma_stage_4		count		Phyllosoma stage 4 count
phyllosoma_stage_5		count		Phyllosoma stage 5 count
phyllosoma_stage_6		count		Phyllosoma stage 6 count
phyllosoma_stage_7		count		Phyllosoma stage 7 count
phyllosoma_stage_8		count		Phyllosoma stage 8 count
phyllosoma_stage_9		count		Phyllosoma stage 9 count
total_phyllosoma		count		Total phyllosoma larvae count
zooplankton_abundance_areal		count/m2	≥ 0	Zooplankton areal abundance (depth-integrated density) per net tow, by higher taxon. Raw (uncorrected).
zooscan_carbon_individual		ugC	≥ 0	Mean individual carbon content from ZooScan optical imaging, by bioclass.
zooscan_feret_diameter		mm	≥ 0	Mean Feret diameter (organism size) from ZooScan optical imaging, by bioclass.
NA
unknown_measurement_1				Unidentified measurement (NaN in every file inspected)
unknown_measurement_2				Unidentified measurement (NaN in every file inspected)

6.4 Life stages and gear

Two more registries — Table 6.4 and Table 6.5 — carry the values that appear on observations and events, each with the Darwin Core label and the NERC concept where one is exact. Two life-stage values are recorded as not life stages (euphausiid damaged, ichthyoplankton invert) and are never published as one.

Table 6.4: Life stages (metadata/life_stage.csv).

life stage	Darwin Core	NERC S11	parent	datasets	note
adult	adult	S1116		cce-lter_euphausiids
calyptopis	calyptopis	S1118		cce-lter_euphausiids
calyptopis C1			calyptopis	cce-lter_euphausiids	S11 has no calyptopis substage; export the verbatim value as lifeStage and the parent's id where a coarser stage is acceptable.
calyptopis C2			calyptopis	cce-lter_euphausiids	S11 has no calyptopis substage.
calyptopis C3			calyptopis	cce-lter_euphausiids	S11 has no calyptopis substage.
damaged				cce-lter_euphausiids	Not a life stage: a BTEDB bucket for specimens too damaged to stage. Belongs in occurrenceRemarks, not lifeStage.
egg	egg	S1122		swfsc_cufes; swfsc_ichthyo
furcilia	furcilia	S1123		cce-lter_euphausiids
furcilia F1			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F2			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F3			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F4			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F5			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F6			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
furcilia F7			furcilia	cce-lter_euphausiids	S11 has no furcilia substage.
invert				swfsc_ichthyo	Not a life stage: marks a record from the merged SWFSC invertebrate counts rather than a fish egg or larva. A taxonomic provenance flag; do not emit as lifeStage.
juvenile	juvenile	S1127		cce-lter_euphausiids
larva	larva	S1128		swfsc_ichthyo
larvae	larva	S1128		cce-lter_euphausiids	BTEDB's plural spelling of the same concept (unstaged larvae); grammatical number is not a facet, so the id is S11's `larva`. The two spellings in one release are a normalization gap on the euphausiid vocabulary.
megalopa	megalopa	S1167		cdfw_dungeness-crab
metanauplius	metanauplius	S1169		cce-lter_euphausiids
phyllosoma				calcofi_phyllosoma	S11 has no phyllosoma concept (the achelatan larval stage); the 11 numbered stages live in obs_attribute as bins.
zoea	zoea	S1137		cdfw_dungeness-crab

Table 6.5: Gear (metadata/gear.csv) — every sample.tow_type code.

code	gear	sampling protocol	NERC L22	datasets
C1	CalCOFI one-metre oblique tow	Oblique tow with a 1-m ring net (1-m mouth diameter, 0.8 m^2 mouth area) retrieved at a constant wire angle from ~140 m to the surface; volume filtered from a flowmeter, abundance standardized per 10 m^2 of sea surface by the standard haul factor.	TOOL0988	swfsc_ichthyo
C2	CalCOFI two-metre oblique tow	Oblique tow with a 2-m^2 mouth-area ring net (1.6-m mouth diameter).		swfsc_ichthyo
CB	CalCOFI oblique bongo tow	Oblique tow with a 71-cm bongo net (0.4 m^2 mouth area per cod end, 0.505 mm mesh) retrieved at a constant 45 degree wire angle from 210 m to the surface; volume filtered from a flowmeter, abundance standardized per 10 m^2 by the standard haul factor. Paired cod ends: one preserved in formalin for SWFSC ichthyoplankton, one for the SIO Pelagic Invertebrate Collection.	NETT0176	swfsc_ichthyo
CV	CalCOFI vertical egg tow	Vertical tow with a 0.25 m^2 mouth-area ring net; abundance standardized per unit sea-surface area.		swfsc_ichthyo
DC	Deep oblique bongo tow	Oblique tow to 600 m with the CB bongo net, historically used to sample sablefish.	NETT0176	swfsc_ichthyo
M1	MOCNESS (1 m^2)	Multiple Opening/Closing Net and Environmental Sensing System, 1 m^2 mouth area.		swfsc_ichthyo
M2	MOCNESS (3 m^2)	Multiple Opening/Closing Net and Environmental Sensing System, 3 m^2 mouth area.		swfsc_ichthyo
MB	MARMAP oblique bongo tow	Oblique tow with a MARMAP bongo net (2-ft mouth diameter).		swfsc_ichthyo
MT	Manta surface tow	Surface (neuston) tow with a twin-winged continuous-flow Manta net; abundance standardized per 1000 m^3 of water strained (volume, not haul factor — a Manta tow has no depth-integrated area).	NETT0177	swfsc_ichthyo
PV	PairoVET vertical egg tow	Paired vertical tows of the CalCOFI vertical egg net (PairoVET), fished from ~70 m to the surface for fish eggs.		swfsc_ichthyo
OBLIQUE	Oblique tow (gear unrecorded)	Oblique tow; the CDFW Dungeness megalopae sorting log records the tow geometry but not the net.		cdfw_dungeness-crab

6.5 Providers, licences and dataset names

A provider is the organization that curates — holds and can license — the data, never the portal that serves it and never a collection or lab inside it. CalCOFI program data is calcofi even when served from NCEI or EDI; the Pelagic Invertebrate Collection is a dataset of provider sio. Every provider an ingest names must be registered in Table 6.6, or the build stops.

Table 6.6: Providers (metadata/provider.csv).

provider	name	url	status	datasets
calcofi	California Cooperative Oceanic Fisheries Investigations	↗	active	9
swfsc	NOAA Southwest Fisheries Science Center	↗	active	2
sio	Scripps Institution of Oceanography, UC San Diego	↗	active	2
cce-lter	California Current Ecosystem Long Term Ecological Research	↗	active	5
cdfw	California Department of Fish and Wildlife	↗	active	1
farallon	Farallon Institute	↗	active	1
sccoos	Southern California Coastal Ocean Observing System	↗	active	0
jcvi	J. Craig Venter Institute	↗	active	0
calpoly	California Polytechnic State University	↗	active	0
stanford	Hopkins Marine Station, Stanford University	↗	active	0

A dataset’s key is {provider}_{dataset}, both slugs lower case with hyphens inside a slug (cce-lter_zooscan, cdfw_dungeness-crab). The key names everything about the dataset: its ingest notebook, its folder of metadata, its row in the provider’s Sheet, its record in the release and its page at calcofi.io/datasets/{key}/. The human names — dataset_name and the short form the apps show — are declared once, in the ingest notebook’s calcofi: block, and every surface reads them from there. This is the nomenclature the data management plan’s Task 13 asks to be agreed; Table 6.7 is the current state of it.

Table 6.7: The datasets of v2026.11.05 — key, names, provider and category.

dataset_key	name	short name	provider	category	license
calcofi_2022-edna	CalCOFI October 2022 Vertebrate eDNA	2022 Vertebrate eDNA	calcofi	Genomics & eDNA	CC-BY-4.0
calcofi_bottle	CalCOFI Bottle Database	Hydrographic Bottle	calcofi	Physical Oceanography	CC-BY-4.0
calcofi_bottle-derived	CalCOFI Bottle Derived Hydrographic Products	Bottle Derived Products	calcofi	Physical Oceanography	CC-BY-4.0
calcofi_ctd-cast	CalCOFI CTD Cast Files	CTD Cast Files	calcofi	Physical Oceanography
calcofi_ctd-derived	CalCOFI CTD Derived Hydrographic Products	CTD Derived Products	calcofi	Physical Oceanography
calcofi_dic	CalCOFI DIC	Carbonate Chemistry / DIC	calcofi	Carbonate System	CC-BY-4.0
calcofi_mets	CalCOFI METS (Underway TSG/Meteorology)	Underway Meteorological (METS)	calcofi	Meteorology & Sea State
calcofi_phyllosoma	CalCOFI Lobster Phyllosoma	Phyllosoma (Lobster Larvae)	calcofi	Zooplankton	custom
calcofi_phytoplankton	CalCOFI Phytoplankton (Venrick)	Phytoplankton	calcofi	Phytoplankton	CC0-1.0
cce-lter_euphausiids	CCE-LTER Euphausiid Abundance	Euphausiids (Krill)	cce-lter	Euphausiids (Krill)	custom
cce-lter_iron	CCE-LTER Dissolved Iron (CalCOFI Cruises)	Dissolved iron	cce-lter	Nutrients & Chemistry	custom
cce-lter_picoplankton-bacteria	Picoplankton and Bacteria Abundance (CalCOFI Cruise)	Picoplankton & Bacteria	cce-lter	Picoplankton & Bacteria
cce-lter_zoodb	ZooDB Holoplankton Community	ZooDB (Holoplankton Community)	cce-lter	Zooplankton	custom
cce-lter_zooscan	ZooScan PRPOOS Zooplankton	ZooScan (Imaged Zooplankton)	cce-lter	Zooplankton	custom
cdfw_dungeness-crab	CDFW Dungeness Crab Megalopae	Dungeness Crab Megalopae	cdfw	Zooplankton	CC-BY-4.0
farallon_bird-mammal	CalCOFI Bird & Mammal Census	Seabirds & Marine Mammals	farallon	Seabirds & Marine Mammals	CC-BY-4.0
sio_mesopelagic-fish	UCSD SIO Mesopelagic Fish	Mesopelagic Fish	sio	Mesopelagic Fish	CC-BY-4.0
sio_pic-zooplankton	SIO PIC Zooplankton Net Tows	Zooplankton Net Tows	sio	Zooplankton
swfsc_cufes	CalCOFI Underway CUFES Fish Eggs	CUFES Fish Eggs	swfsc	Fish Eggs & Larvae	custom
swfsc_ichthyo	SWFSC Ichthyoplankton	Ichthyoplankton	swfsc	Fish Eggs & Larvae

A dataset’s license is one of the ids in Table 6.8, and nothing else is accepted. One of the ids, unknown, means the licence is pending: the source states none and the provider has been asked. A dataset carrying it shows unknown in Table 6.7, its citation may be empty for the same reason, and check_dataset_citation() lets it through only while an open question on the license field names the gap — no licence is ever invented to fill it, and none is implied for reuse until the provider answers.

Table 6.8: Licence ids a dataset may declare (metadata/license.csv); custom needs a license_url.

license	name	url	status	notes
CC-BY-4.0	Creative Commons Attribution 4.0 International	↗	active	Attribution required. Declared by calcofi_dic (NCEI rightsList), sio_mesopelagic-fish, cdfw_dungeness-crab and farallon_bird-mammal (its 2025-07-23 data-sharing agreement); proposed for the calcofi.org-hosted program data (bottle Q10, ctd-cast Q28, mets Q29).
CC0-1.0	CC0 1.0 Universal (public domain dedication)	↗	active	No rights reserved; attribution is etiquette, not a condition. calcofi_phytoplankton (EDI knb-lter-cce.254 intellectualRights).
CC-BY-NC-4.0	Creative Commons Attribution-NonCommercial 4.0 International	↗	active	Non-commercial use only. No dataset declares it yet.
CC-BY-SA-4.0	Creative Commons Attribution-ShareAlike 4.0 International	↗	active	No dataset declares it yet.
US-PD	US Government work (public domain)	↗	active	17 U.S.C. § 105: a work of the United States Government is not subject to copyright. Proposed for swfsc_ichthyo (Q11).
custom	Custom terms stated by the provider		active	Requires `license_url` pointing at the provider's own terms — an EDI intellectualRights page, a portal's Data Use Policy, an ERDDAP .das `license` global, a data-sharing agreement. The index and the release fail without the URL. Declared by phyllosoma, euphausiids, zoodb, zooscan, cufes (farallon moved to CC-BY-4.0 on 2026-10-21: its data-sharing agreement states CC BY 4.0).
unknown	Not yet established		active	Fails the index and the release unless an open/proposed questions.csv row with related_table = dataset covers `license`. An empty license is treated the same way; prefer leaving the field empty with the question filed.

6.6 Legacy names, mapped

Every dataset arrived with its own names, and every one of them is recorded: the dictionary’s aliases column lists what each standard field was called in the sources, and each ingest keeps a crosswalk, metadata/{provider}/{dataset}/flds_redefine.csv, from every source column to its standard name and type. Nothing is renamed in a source file; the mapping is applied at ingest and kept so the provider’s own names remain answerable; Table 6.9 counts them per dataset.

Table 6.9: Each dataset’s crosswalk — how many source fields it maps, and how many change name on the way in. The full crosswalk per dataset follows (HTML), and each is a CSV in CalCOFI/workflows.

dataset_key	fields	renamed	crosswalk
calcofi_2022-edna	18	15	flds_redefine.csv
calcofi_bottle	123	123	flds_redefine.csv
calcofi_ctd-cast	6	5	flds_redefine.csv
calcofi_ctd-derived	13	0	flds_redefine.csv
calcofi_dic	18	18	flds_redefine.csv
calcofi_mets	101	97	flds_redefine.csv
calcofi_phyllosoma	25	21	flds_redefine.csv
cce-lter_euphausiids	12	12	flds_redefine.csv
cce-lter_iron	21	10	flds_redefine.csv
cce-lter_picoplankton-bacteria	23	12	flds_redefine.csv
cce-lter_zoodb	17	6	flds_redefine.csv
cce-lter_zooscan	13	3	flds_redefine.csv
cdfw_dungeness-crab	35	35	flds_redefine.csv
farallon_bird-mammal	39	39	flds_redefine.csv
sio_mesopelagic-fish	21	19	flds_redefine.csv
sio_pic-zooplankton	20	20	flds_redefine.csv
swfsc_cufes	27	27	flds_redefine.csv
swfsc_ichthyo	101	98	flds_redefine.csv

calcofi_2022-edna

source name	standard name	source type	type	units
edna_assay
target_gene	assay		varchar
scientificNameID	ds_taxa_code		varchar
organismQuantity	reads		bigint
(derived from scientificNameID)	worms_id		integer
edna_context
measurementType	measurement_type		varchar
measurementValue	measurement_value		double
edna_detection
(derived)	n_library		integer
organismQuantity	reads		bigint
edna_sample
eventDate	datetime_start_utc		timestamp
maximumDepthInMeters	depth_max_m		decimal
minimumDepthInMeters	depth_min_m		decimal
decimalLatitude	latitude		decimal
locationID	location_id		varchar
decimalLongitude	longitude		decimal
parentEventID	parent_event_id		varchar

calcofi_bottle

source name	standard name	source type	type	units
bottle
Btl_Cnt	bottle_id	numeric	integer
BtlNum	btl_num	numeric	smallint
C14A1p	c14a1p	numeric	decimal
C14A1q	c14a1q	character	varchar
C14A2p	c14a2p	numeric	decimal
C14A2q	c14a2q	character	varchar
C14As1	c14as1	numeric	decimal	milligrams C per cubic meter per half light day
C14As2	c14as2	numeric	decimal	milligrams C per cubic meter per half light day
Cst_Cnt	cast_id	numeric	integer
ChlorA	chlor_a	numeric	decimal	micrograms per liter
Chlqua	chlqua	character	varchar
DarkAp	dark_ap	numeric	decimal
DarkAs	dark_as	numeric	decimal	milligrams C per cubic meter per half light day
DarkAq	darkaq	character	varchar
Depth_ID	depth_key	character	varchar
Depthm	depth_m	numeric	decimal	meters
DIC1	dic1	numeric	decimal	micromoles per kilogram
DIC2	dic2	numeric	decimal	micromoles per kilogram
DIC Quality Comment	dic_quality_comment	character	varchar
IncTim	inc_tim	character	varchar
LightP	light_p	numeric	decimal	percent
MeanAp	mean_ap	numeric	decimal
MeanAq	mean_aq	character	varchar
MeanAs	mean_as	numeric	decimal	milligrams C per cubic meter per half light day
NH3q	nh3q	character	varchar
NH3uM	nh3u_m	numeric	decimal	micromoles per liter
NO2q	no2q	character	varchar
NO2uM	no2u_m	numeric	decimal	micromoles per liter
NO3q	no3q	character	varchar
NO3uM	no3u_m	numeric	decimal	micromoles per liter
O2ml_L	o2ml_l	numeric	decimal	milliliters per liter
O2Sat	o2sat	numeric	decimal	percent saturation
O2Satq	o2satq	character	varchar
O_qual	o_qual	character	varchar
Oxy_µmol/Kg	oxy_umol_kg	numeric	decimal	micromoles per kilogram
pH1	p_h1	numeric	decimal	pH scale
pH2	p_h2	numeric	decimal	pH scale
P_qual	p_qual	character	varchar
Phaeop	phaeop	numeric	decimal	micrograms per liter
Phaqua	phaqua	character	varchar
PO4q	po4q	character	varchar
PO4uM	po4u_m	numeric	decimal	micromoles per liter
R_Depth	r_depth	numeric	decimal	meters
R_DYNHT	r_dynht	numeric	decimal	dynamic meters
R_Nuts	r_nuts	numeric	decimal	micromoles per liter
R_Oxy_µmol/Kg	r_oxy_umol_kg	numeric	decimal	micromoles per kilogram
R_Sal	r_sal	numeric	decimal	Specific Volume Anomaly
R_TEMP	r_temp	numeric	decimal	degrees Celsius
RecInd	rec_ind	character	varchar
S_prec	s_prec	numeric	decimal
S_qual	s_qual	character	varchar
STheta	s_theta	numeric	decimal	kilograms per cubic meter
SThtaq	s_thtaq	character	varchar
Salnty	salnty	numeric	decimal	Practical Salinity Scale
SiO3qu	si_o3qu	character	varchar
SiO3uM	si_o3u_m	numeric	decimal	micromoles per liter
Sta_ID	site_key	character	varchar
T_degC	t_deg_c	numeric	decimal	degrees Celsius
T_prec	t_prec	numeric	decimal
T_qual	t_qual	character	varchar
TA1	ta1	numeric	decimal	micromoles per kilogram
TA2	ta2	numeric	decimal	micromoles per kilogram
casts
Ac_Line	ac_line	numeric	decimal
Ac_Sta	ac_sta	numeric	decimal
Barometer	barometer	numeric	decimal	millibars
Bottom_D	bottom_depth_m	numeric	decimal	meters
Cst_Cnt	cast_id	numeric	integer
Cast_ID	cast_key	character	varchar
Civil_T	civil_t	character	varchar
Cloud_Amt	cloud_amt	numeric	smallint
Cloud_Typ	cloud_typ	numeric	smallint
Cruise	cruise	character	varchar
Cruise_ID	cruise_key_0	character	varchar
Cruz_Leg	cruz_leg	character	varchar
Cruz_Num	cruz_num	character	varchar
Cruz_Sta	cruz_sta	character	varchar
Data_Or	data_or	character	varchar
Data_Type	data_type	character	varchar
Date	date	character	date
DbSta_ID	db_sta_key	character	varchar
Distance	distance	numeric	decimal	nautical miles
Dry_T	dry_t	numeric	decimal	degrees Celsius
Event_Num	event_num	numeric	smallint
ForelU	forel_u	numeric	smallint	Forel-Ule Scale
Inc_End	inc_end	character	varchar
Inc_Str	inc_str	character	varchar
IntC14	int_c14	numeric	decimal	milligrams C per square meter per half light day
IntChl	int_chl	numeric	decimal	milligrams chl per square meter per half light day
Julian_Date	julian_date	numeric	decimal
Julian_Day	julian_day	numeric	smallint
Lat_Deg	lat_deg	numeric	smallint	degrees
Lat_Hem	lat_hem	character	varchar
Lat_Min	lat_min	numeric	decimal	minutes
Lat_Dec	latitude	numeric	decimal	decimal_degrees
Lon_Deg	lon_deg	numeric	smallint	degrees
Lon_Hem	lon_hem	character	varchar
Lon_Min	lon_min	numeric	decimal	minutes
Lon_Dec	longitude	numeric	decimal	decimal_degrees
Month	month	numeric	smallint
Order_Occ	order_occ	numeric	smallint
Orig_Sta_ID	orig_sta_id	character	varchar
PST_LAN	pst_lan	character	varchar
Quarter	quarter	numeric	smallint
Rpt_Line	rpt_line	numeric	decimal
Rpt_Sta	rpt_sta	numeric	decimal
Secchi	secchi	numeric	decimal	meters
Ship_Code	ship_code	character	varchar
Ship_Name	ship_name	character	varchar
Sta_ID	site_key	character	varchar
St_Line	st_line	numeric	decimal
St_Station	st_station	numeric	decimal
Sta_Code	sta_code	character	varchar
Time	time	character	varchar
TimeZone	time_zone	numeric	smallint
Visibility	visibility	numeric	smallint
Wave_Dir	wave_dir	numeric	smallint	degrees
Wave_Ht	wave_ht	numeric	decimal	feet
Wave_Prd	wave_prd	numeric	smallint	seconds
Wea	wea	numeric	smallint
Wet_T	wet_t	numeric	decimal	degrees Celsius
Wind_Dir	wind_dir	numeric	smallint	degrees
Wind_Spd	wind_spd	numeric	decimal	knots
Year	year	numeric	smallint

calcofi_ctd-cast

source name	standard name	source type	type	units
ctd_cast
cast_id	cast_key		varchar
lat_dec	latitude		decimal
lon_dec	longitude		decimal
sta_id	site_key		varchar
ctd_measurement
depth	depth_m		decimal

calcofi_ctd-derived

Every source field keeps its name.

calcofi_dic

source name	standard name	source type	type	units
dic_sample
CTDTEMP_ITS90	ctdtemp	character	double	deg_C
CTDTEMP_flag	ctdtemp_flag	numeric	smallint
Day_UTC	day_utc	numeric	smallint
Depth	depth_m	character	double	m
DIC	dic	character	double	umol/kg
DIC_flag	dic_flag	numeric	smallint
EXPOCODE	expocode	character	varchar
Latitude	latitude	character	double	decimal degrees
Longitude	longitude	character	double	decimal degrees
Month_UTC	month_utc	numeric	smallint
Salinity_PSS78	salinity	numeric	double	PSS-78
Salinity_flag	salinity_flag	numeric	smallint
Ship_Name	ship_name	character	varchar
Station_ID	site_key	character	varchar
TA	ta	character	double	umol/kg
TA_flag	ta_flag	numeric	smallint
Time_UTC	time_utc	character	time
Year_UTC	year_utc	numeric	smallint

calcofi_mets

source name	standard name	source type	type	units
mets_sample
AirTemp	air_temp_c	numeric	double	deg_C
AtmPress	atm_pressure_mb	numeric	double	mb
AtmPres	atm_pressure_mb	numeric	double	mb
AtmPress_SLC	atm_pressure_slc_mb	numeric	double	mb
BottomDepth	bottom_depth_m	numeric	double	m
BottomDepth_MB	bottom_depth_mb_m	numeric	double	m
Fluor_UG/L	chl_fluor	numeric	double	ug/L
ChlFluor	chl_fluor	numeric	double
COG	course_over_ground_deg	numeric	double	degrees
Cruise	cruise_orig	character	varchar
col_1	date_mdy	character	varchar
DATE_PST	date_pst	character	varchar
col_1	date_ymd	character	varchar
DATE_TIME_UTC	datetime_start_utc	numeric	timestamp
DateTime	datetime_start_utc	numeric	timestamp
DIC_pCO2_raw	dic_pco2_raw	numeric	double
DIC_pH_raw	dic_ph_raw	numeric	double
DIC_Sal	dic_salinity_psu	numeric	double	PSU
DIC_Temp	dic_temp_c	numeric	double	deg_C
DIC_valve	dic_valve	numeric	double
Heading	heading_deg	numeric	double	degrees
Latitude_N	latitude	numeric	double	decimal_degrees
Lat	latitude	numeric	double	decimal_degrees
col_4	latitude	numeric	double	decimal_degrees
LA	latitude	numeric	double	decimal_degrees
LongWaveRad	long_wave_rad	numeric	double	W/m2
Longitude_W	longitude	numeric	double	decimal_degrees
Lon	longitude	numeric	double	decimal_degrees
col_5	longitude	numeric	double	decimal_degrees
LO	longitude	numeric	double	decimal_degrees
Oxygen	oxygen	numeric	double
OxygenSat	oxygen_sat_pct	numeric	double	percent
OxygenTemp	oxygen_temp_c	numeric	double	deg_C
PARSurf	par_surf	numeric	double
Est_CHLA_UG/L	pred_chl	numeric	double	ug/L
Pred_Chl	pred_chl	numeric	double
Pred_Sal	pred_sal_psu	numeric	double
Pred_TSGSal	pred_sal_psu	numeric	double
Pred_SST	pred_sst_c	numeric	double
Pred_SSTemp	pred_sst_c	numeric	double
Pred_Temp	pred_temp_c	numeric	double
Pred_TSGTemp	pred_temp_c	numeric	double
RelHum	rel_humidity_pct	numeric	double	percent
ShortWaveRad	short_wave_rad	numeric	double	W/m2
ID	source_row_id	numeric	integer
SOG	speed_over_ground_kt	numeric	double	knots
SSCond	ss_conductivity	numeric	double	S/m
Salinity_PSU	sss_psu	numeric	double	PSU
SSSal	sss_psu	numeric	double	PSU
Corr_SAL_PSU	sss_psu_corrected	numeric	double	PSU
SST_degC	sst_c	numeric	double	deg_C
SSTemp	sst_c	numeric	double	deg_C
Corr_SST_degC	sst_c_corrected	numeric	double	deg_C
SW_pH	sw_ph	numeric	double
col_2	time_hms	character	varchar
col_2	time_hms_ms	character	varchar
TIME_PST	time_pst	character	varchar
TransV	transmissometer_v	numeric	double	V
TSG_Cond	tsg1_conductivity	numeric	double	S/m
col_4	tsg1_conductivity	numeric	double	S/m
TSG_Dens	tsg1_density	numeric	double	kg/m3
TSG_Sal	tsg1_salinity_psu	numeric	double	PSU
TSGSal	tsg1_salinity_psu	numeric	double	PSU
col_7	tsg1_salinity_psu	numeric	double	PSU
col_5	tsg1_salinity_psu	numeric	double	PSU
SA	tsg1_salinity_psu	numeric	double	PSU
CAL_S	tsg1_salinity_psu_calibrated	numeric	double	PSU
SoundVel	tsg1_sound_velocity	numeric	double	m/s
TSG_Temp	tsg1_temp_c	numeric	double	deg_C
TSGTemp	tsg1_temp_c	numeric	double	deg_C
col_6	tsg1_temp_c	numeric	double	deg_C
col_3	tsg1_temp_c	numeric	double	deg_C
ST	tsg1_temp_c	numeric	double	deg_C
CAL_T	tsg1_temp_c_calibrated	numeric	double	deg_C
TSG_Cond_2	tsg2_conductivity	numeric	double	S/m
TSG_Dens_2	tsg2_density	numeric	double	kg/m3
TSG_Sal_2	tsg2_salinity_psu	numeric	double	PSU
SoundVel_2	tsg2_sound_velocity	numeric	double	m/s
TSG_Temp_2	tsg2_temp_c	numeric	double	deg_C
TSG_Temp2	tsg2b_temp_c	numeric	double	deg_C
TSG_Cond_3	tsg3_conductivity	numeric	double	S/m
TSG_Dens_3	tsg3_density	numeric	double	kg/m3
TSG_Sal_3	tsg3_salinity_psu	numeric	double	PSU
SoundVel_3	tsg3_sound_velocity	numeric	double	m/s
TSG_Temp_3	tsg3_temp_c	numeric	double	deg_C
TSG_Cond_5	tsg5_conductivity	numeric	double	S/m
TSG_Dens_5	tsg5_density	numeric	double	kg/m3
TSG_Sal_5	tsg5_salinity_psu	numeric	double	PSU
SoundVel_5	tsg5_sound_velocity	numeric	double	m/s
TSG_Temp_5	tsg5_temp_c	numeric	double	deg_C
col_3	unknown_counter	numeric	double
col_8	unknown_measurement_1	numeric	double
col_9	unknown_measurement_2	numeric	double
Flowmeter_LPM	uws_flow	numeric	double	L/min
USWFlow	uws_flow	numeric	double
WindDir	wind_dir_deg	numeric	double	degrees
WindSpeed	wind_speed_ms	numeric	double	m/s
DATE_UTC		numeric
TIME_UTC		numeric
Date		numeric
Time		numeric

calcofi_phyllosoma

source name	standard name	source type	type	units
phyllosoma_measurement
stage_1	phyllosoma_stage_1		INTEGER	count
stage_10	phyllosoma_stage_10		INTEGER	count
stage_11	phyllosoma_stage_11		INTEGER	count
stage_2	phyllosoma_stage_2		INTEGER	count
stage_3	phyllosoma_stage_3		INTEGER	count
stage_4	phyllosoma_stage_4		INTEGER	count
stage_5	phyllosoma_stage_5		INTEGER	count
stage_6	phyllosoma_stage_6		INTEGER	count
stage_7	phyllosoma_stage_7		INTEGER	count
stage_8	phyllosoma_stage_8		INTEGER	count
stage_9	phyllosoma_stage_9		INTEGER	count
phyllosoma_tow
aliquot_adjustment_value	aliquot_adjustment		VARCHAR
aliquot_percent	aliquot_pct		DOUBLE	percent
year_month_of_tow	cruise_orig		VARCHAR
tow_collection_day	date		DATE
latitude_o	latitude		DOUBLE	decimal_degrees
station_line	line		DOUBLE
longitude_o	longitude		DOUBLE	decimal_degrees
ship	ship_name		VARCHAR
station_number	station		DOUBLE
volume_water_filtered_ml_1000m3	volume_filtered		DOUBLE	ml/1000m3

cce-lter_euphausiids

source name	standard name	source type	type	units
euphausiids_taxon
{Genus}{species}{life_stage}_Abundance	scientific_name + life_stage	numeric	DOUBLE	numberPerMeterSquared
euphausiids_tow
Cruise	cruise_orig	character	VARCHAR
Date	date	Date	DATE
TowEnd	datetime_end_utc	timestamp	TIMESTAMP
TowBegin	datetime_start_utc	character	TIMESTAMP
Latitude	latitude	numeric	DOUBLE	decimal_degrees
Line	line	character	DOUBLE
Longitude	longitude	numeric	DOUBLE	decimal_degrees
Region	region	character	VARCHAR
Ship	ship_name	character	VARCHAR
Station	station	character	DOUBLE
RowNumber	tow_id	numeric	INTEGER

cce-lter_iron

source name	standard name	source type	type	units
iron_measurement
Dissolved Fe (nM/L)		VARCHAR		nmol/L
Total Fe (nM/L)		VARCHAR		nmol/L
Chla response to Fe+		VARCHAR
iron_sample
Datetime PST	datetime_start_utc	VARCHAR	TIMESTAMP
Depth (m)	depth_m	VARCHAR	DOUBLE	m
Event Number	event_number	VARCHAR	DOUBLE
Index Number	index_number	VARCHAR	INTEGER
Iron Sampling Equipment	iron_sampling_equipment	VARCHAR	VARCHAR
Latitude (º)	latitude	VARCHAR	DOUBLE	decimal_degrees
Line	line	VARCHAR	DOUBLE
Longitude (º)	longitude	VARCHAR	DOUBLE	decimal_degrees
Station	station	VARCHAR	DOUBLE
studyName	study_name	VARCHAR	VARCHAR

cce-lter_picoplankton-bacteria

source name	standard name	source type	type	units
picoplankton_bacteria_bottle
Associated Bottle Number	assoc_bottle_number	VARCHAR	INTEGER
Bottle Number	bottle_number	VARCHAR	INTEGER
Cast Number	cast_number	VARCHAR	INTEGER
Cruise	cruise_code	VARCHAR	VARCHAR
Datetime GMT	datetime_utc	VARCHAR	TIMESTAMP
Depth (m)	depth_m	VARCHAR	DOUBLE	m
Latitude (º)	latitude	VARCHAR	DOUBLE	decimal_degrees
Line	line	VARCHAR	DOUBLE
Longitude (º)	longitude	VARCHAR	DOUBLE	decimal_degrees
Notes	notes	VARCHAR	VARCHAR
Station	station	VARCHAR	DOUBLE
studyName	study_name	VARCHAR	VARCHAR
picoplankton_bacteria_measurement
Heterotrophic Bacteria (number/ml)		VARCHAR		number/ml
Prochlorococcus (number/ml)		VARCHAR		unconfirmed (see Q01)
Synechococcus (number/ml)		VARCHAR		number/ml
Picoeukaryotes (number/ml)		VARCHAR		number/ml

cce-lter_zoodb

source name	standard name	source type	type	units
zoodb_measurement
abundance_per_1000m3	measurement_value		DOUBLE
zoodb_sample
cruise	cruise_orig		VARCHAR
tow_end	datetime_end_utc		TIMESTAMP
tow_begin	datetime_start_utc		TIMESTAMP
ship	ship_name		VARCHAR
zoodb_taxon
taxon	taxon_slug		VARCHAR

cce-lter_zooscan

source name	standard name	source type	type	units
zooscan_measurement
abundance_per_m2	measurement_value		DOUBLE
zooscan_sample
cruise	cruise_orig		VARCHAR
zooscan_taxon
taxon	taxon_slug		VARCHAR

cdfw_dungeness-crab

source name	standard name	source type	type	units
dungeness_carapace
Carapace length	carapace_length_mm		DOUBLE	mm
dungeness_measurement
Dungeness Crab Megalopae	measurement_value		DOUBLE	count
Other Megalopae	measurement_value		DOUBLE	count
Cancer Zoea	measurement_value		DOUBLE	count
Other Zoea	measurement_value		DOUBLE	count
Description	taxa_description		VARCHAR
dungeness_sample
Aliq.	aliquot		DOUBLE	fraction
Sample Comments	comments		VARCHAR
Cruise	cruise_orig		VARCHAR
Date	date		DATE
Line	line		DOUBLE
Order_Occ	order_occ		SMALLINT
Station	station		DOUBLE
Time	time_sec		INTEGER	s
Vol (ml)	volume_ml		DOUBLE	ml
dungeness_sorting_log
SampleDate	date		DATE
Expedition	expedition_orig		VARCHAR
Lat	latitude		DOUBLE	decimal_degrees
Staline	line		DOUBLE
Lon	longitude		DOUBLE	decimal_degrees
MaxDepth	max_depth_m		DOUBLE	m
Mesh	mesh_mm		DOUBLE	mm
Net	net		VARCHAR
Preservative	preservative		VARCHAR
StaNo	station		DOUBLE
EndTime	time_end_sec		INTEGER	s
StartTime	time_start_sec		INTEGER	s
Tow	tow_type		VARCHAR
dungeness_specimen
Size mm (rostrum to end of carapace)	carapace_length_mm		DOUBLE	mm
CR	cruise_orig		VARCHAR
Sample Date	date		DATE
Dungeness Crab megalopae?	is_magister		BOOLEAN
Notes	notes		VARCHAR
Station	station		DOUBLE
Time	time_sec		INTEGER	s

farallon_bird-mammal

source name	standard name	source type	type	units
bird_mammal_behavior
Behavior	behavior		VARCHAR
ID	behavior_code		VARCHAR
Description	description		VARCHAR
bird_mammal_observation
Behavior	behavior_code		VARCHAR
Count	count		INTEGER	count
GIS key	gis_key		VARCHAR
Species	species_code		VARCHAR
bird_mammal_species
Comment	comment		VARCHAR
Common Name	common_name		VARCHAR
Include	include_flag		BOOLEAN
Bird	is_bird		BOOLEAN
Fish	is_fish		BOOLEAN
LargeBird	is_large_bird		BOOLEAN
Mammal	is_mammal		BOOLEAN
Unidentified	is_unidentified		BOOLEAN
ITIS	itis_id		INTEGER
NMFS	nmfs_code		VARCHAR
Latin Name	scientific_name		VARCHAR
Species	species_code		VARCHAR
bird_mammal_transect
Area (m²)	area_m2		DOUBLE	m2
Bin number	bin_number		INTEGER
Depth (m)	bottom_depth_m		DOUBLE	m
Cruise	cruise_label		VARCHAR
Date	date		DATE
GIS key	gis_key		VARCHAR
Julian date	julian_date		DOUBLE
Julian day	julian_day		INTEGER
Latitude Mid (º)	latitude		DOUBLE	decimal_degrees
Latitude Start (º)	latitude_start		DOUBLE	decimal_degrees
Latitude Stop (º)	latitude_stop		DOUBLE	decimal_degrees
Length (m)	length_m		DOUBLE	m
Longitude Mid (º)	longitude		DOUBLE	decimal_degrees
Longitude Start (º)	longitude_start		DOUBLE	decimal_degrees
Longitude Stop (º)	longitude_stop		DOUBLE	decimal_degrees
Season	season		VARCHAR
SVY	svy		VARCHAR
Time (sec)	time_sec		DOUBLE	s
Transect number	transect_number		INTEGER
Width (m)	width_m		DOUBLE	m

sio_mesopelagic-fish

source name	standard name	source type	type	units
mesopelagic_fish_measurement
<pivoted value>	measurement_value	DOUBLE	DOUBLE	count
<91 species columns + UnidentifiedFish>	scientific_name	VARCHAR	VARCHAR
mesopelagic_fish_tow
Time Zone	(used to derive datetime_start_utc	not stored)	VARCHAR	Explicit PST/PDT per tow from the ‘Original’ sheet – genuinely DST-aware, not assumed.
CruiseID	cruise_key	INTEGER	VARCHAR
Date of Tow	date_of_tow	DATE	DATE
(derived)	datetime_start_utc		TIMESTAMP
CalDepth	depth_m	DOUBLE	DOUBLE	m
(derived)	hour_source_conflict		BOOLEAN
LatFinal	latitude	DOUBLE	DOUBLE	decimal_degrees
LongFinal	longitude	DOUBLE	DOUBLE	decimal_degrees
(derived)	site_key		VARCHAR
Station	station_raw	DOUBLE	VARCHAR
Time	tow_hour	DOUBLE	INTEGER
Start hour;Start Minute	tow_hour;tow_minute (via datetime_start_utc)	INTEGER	INTEGER
Time	tow_minute	DOUBLE	INTEGER
Month	tow_month	INTEGER	INTEGER
Tow	tow_number	INTEGER	INTEGER
Year	tow_year	INTEGER	INTEGER
VolFilt	volume_sampled	DOUBLE	DOUBLE	m3
DensityTotal		DOUBLE
Abundance		DOUBLE

sio_pic-zooplankton

source name	standard name	source type	type	units
zooplankton_tow
SAMPLE_DATE_pnt	date	character	DATE
END_TIME_pnt	datetime_end_utc	character	TIMESTAMP
START_TIME_pnt	datetime_start_utc	character	TIMESTAMP
DEPTH_MAX_pnt	depth_max_m	numeric	DOUBLE	m
DEPTH_MIN_pnt	depth_min_m	numeric	DOUBLE	m
EXPEDITION_pnt	expedition	character	VARCHAR
EXPED_CODE_pnt	expedition_code	character	VARCHAR
Expedition_Type_pnt	expedition_type	character	VARCHAR
FIXATIVE_pnt	fixative	character	VARCHAR
LAT_DECIMAL_pnt	latitude	numeric	DOUBLE	decimal_degrees
STATION_LINE_pnt	line	character	DOUBLE
LONG_DECIMAL_pnt	longitude	numeric	DOUBLE	decimal_degrees
MAX_MWO_pnt	max_wire_out_m	numeric	DOUBLE	m
MESH_SIZE_pnt	mesh_size_mm	numeric	DOUBLE	mm
NET_TYPE_pnt	net_type	character	VARCHAR
SWFOrder_Occ	order_occ	numeric	SMALLINT
PRESERVATIVE_pnt	preservative	character	VARCHAR
SHIP_pnt	ship_name	character	VARCHAR
STATION_NUMBER_pnt	station	character	DOUBLE
TOW_TYPE_pnt	tow_type	character	VARCHAR

swfsc_cufes

source name	standard name	source type	type	units
cufes
AnchovyEggs	anchovy_eggs		INTEGER	count
Cruise	cruise		VARCHAR
CruiseId	cruise_uuid		UUID
CufesId	cufes_uuid		UUID
Stop	datetime_end_utc		TIMESTAMP
Start	datetime_start_utc		TIMESTAMP
HakeEggs	hake_eggs		INTEGER	count
JackMackerelEggs	jack_mackerel_eggs		INTEGER	count
OtherFishEggs	other_fish_eggs		INTEGER	count
SampleNumber	sample_number		INTEGER
SardineEggs	sardine_eggs		INTEGER	count
Ship	ship_key		VARCHAR
SquidEggs	squid_eggs		INTEGER	count
StartLatitude	start_latitude		DOUBLE	decimal_degrees
StartLongitude	start_longitude		DOUBLE	decimal_degrees
StartPumpSpeed	start_pump_speed		DOUBLE	m3/min
StartSalinity	start_salinity		DOUBLE	PSS-78
StartTemperature	start_temperature		DOUBLE	degC
StartWindDirection	start_wind_direction		DOUBLE	degrees
StartWindSpeed	start_wind_speed		DOUBLE	knots
StopLatitude	stop_latitude		DOUBLE	decimal_degrees
StopLongitude	stop_longitude		DOUBLE	decimal_degrees
StopPumpSpeed	stop_pump_speed		DOUBLE	m3/min
StopSalinity	stop_salinity		DOUBLE	PSS-78
StopTemperature	stop_temperature		DOUBLE	degC
StopWindDirection	stop_wind_direction		DOUBLE	degrees
StopWindSpeed	stop_wind_speed		DOUBLE	knots

swfsc_ichthyo

source name	standard name	source type	type	units
cruise
CruiseId	cruise_uuid	character	uuid
Cruise	date_ym	numeric	date
Ship	ship_key	character	varchar
cufes
AnchovyEggs	anchovy_eggs	numeric	decimal
Cruise	cruise	numeric	decimal
CruiseId	cruise_uuid	character	varchar
CufesId	cufes_uuid	character	varchar
HakeEggs	hake_eggs	numeric	decimal
JackMackerelEggs	jack_mackerel_eggs	numeric	decimal
OtherFishEggs	other_fish_eggs	numeric	decimal
SampleNumber	sample_number	numeric	decimal
SardineEggs	sardine_eggs	numeric	decimal
Ship	ship	character	varchar
SquidEggs	squid_eggs	numeric	decimal
Start	start	POSIXct	timestamp
StartLatitude	start_latitude	numeric	decimal
StartLongitude	start_longitude	numeric	decimal
StartPumpSpeed	start_pump_speed	numeric	decimal
StartSalinity	start_salinity	numeric	decimal
StartTemperature	start_temperature	numeric	decimal
StartWindDirection	start_wind_direction	numeric	decimal
StartWindSpeed	start_wind_speed	numeric	decimal
Stop	stop	POSIXct	timestamp
StopLatitude	stop_latitude	numeric	decimal
StopLongitude	stop_longitude	numeric	decimal
StopPumpSpeed	stop_pump_speed	numeric	decimal
StopSalinity	stop_salinity	numeric	decimal
StopTemperature	stop_temperature	numeric	decimal
StopWindDirection	stop_wind_direction	numeric	decimal
StopWindSpeed	stop_wind_speed	numeric	decimal
egg
CountId	count_uuid	character	uuid
NetId	net_uuid	character	uuid
SppCode	species_id	numeric	smallint
Tally	tally	numeric	integer	count
egg_stage
NetId	net_uuid	character	uuid
SppCode	species_id	numeric	smallint
Stage	stage	numeric	smallint
Tally	tally	numeric	integer	count
fish
NetId	net_uuid	character	uuid
SppCode	species_id	numeric	smallint
Tally	tally	numeric	integer	count
invert
NetId	net_uuid	character	uuid
SppCode	species_id	numeric	smallint
Tally	tally	numeric	integer	count
larva
CountId	count_uuid	character	uuid
NetId	net_uuid	character	uuid
SppCode	species_id	numeric	smallint
Tally	tally	numeric	integer	count
larva_measured
CountId	count_uuid	character	uuid
LarvaeId	larva_measured_uuid	character	uuid
Len	length_mm	numeric	decimal	mm
Stage	stage	character	varchar
Tally	tally	numeric	integer	count
net
NetDepth	net_depth_m	numeric	decimal	m
NetId	net_uuid	character	uuid
PropSorted	prop_sorted	numeric	decimal	proportion
NetSide	side	character	varchar
SmallPlankton	smallplankton	numeric	decimal	mL
Shf	standard_haul_factor	numeric	decimal	dimensionless
TotalPlankton	totalplankton	numeric	decimal	mL
TowId	tow_uuid	character	uuid
Vol	volume_sampled	numeric	decimal	m3
preservative
PreservCode	preserv_code	numeric	smallint
Preservative	preservative	character	varchar
ship
ShipIces	ship_ices	character	varchar
Ship	ship_key	character	varchar
ShipName	ship_name	character	varchar
ShipNodc	ship_nodc	character	varchar
site
Arrival	arrival_utc	POSIXct	timestamp
BottomDepth	bottom_depth	numeric	decimal
BucketTemp	bucket_temp	numeric	decimal
CruiseId	cruise_uuid	character	uuid
Departure	departure_utc	POSIXct	timestamp
latidude	latitude	numeric	decimal	decimal_degrees
Line	line	numeric	decimal
OrderOcc	order_occ	numeric	smallint
StationId	site_uuid	character	uuid
Station	station	numeric	decimal
species
CommonName	common_name	character	varchar
Tsn	itis_id	numeric	integer
Taxon	scientific_name	character	varchar
SppCode	species_id	numeric	smallint
AphiaId	worms_id	numeric	integer
species_itis
Tsn	itis_id	numeric	integer
ParentTsn	parent_itis_id	numeric	integer
Taxon	taxon	character	varchar
TaxonRank	taxon_rank	character	varchar
TaxonRankId	taxon_rank_id	numeric	smallint
species_worms
parent_aphia_id	parent_worms_id	numeric	integer
Taxon	taxon	character	varchar
AphiaId	worms_id	numeric	integer
tow
TowStartTime	datetime_start_utc	POSIXct	timestamp
StationId	site_uuid	character	uuid
TowNumber	tow_number	numeric	smallint
TowType	tow_type_key	character	varchar
TowId	tow_uuid	character	uuid
tow_type
Description	description	character	varchar
TowType	tow_type_key	character	varchar

6.7 Proposing a change

A convention changes the way the data does: through a pull request to metadata/ in CalCOFI/workflows — a row in the dictionary (authored in libs/build_field_dictionary.R, which regenerates the CSV), a measurement type registered with calcofi4db::register_measurement_types(), a life stage or gear row — or, where the question is the provider’s to answer, a row in that dataset’s questions.csv and its Sheet (Metadata & the ingest loop). The next release carries whatever changed, and this page follows.