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 (61 of 61 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; FK to grid. Assigned spatially via assign_grid_key().
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
ship_code	VARCHAR		Source ship code as provided by the data provider; resolve to ship_key.	Ship_Code
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
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
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
date_max	DATE		Last event date observed for a cruise (from its own tows).
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

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	95	2
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)	14	0
Carbonate System	env	Dissolved inorganic carbon, alkalinity, pH and pCO2	15	1
Productivity & Pigments	env	Chlorophyll a, phaeopigments, primary production (C14) and light (PAR)	17	0
Meteorology & Sea State	env	Wind, air temperature, pressure, cloud, visibility, sea state and water colour from the underway METS and ship observations	16	1
Phytoplankton	bio	Phytoplankton counts by taxon or functional group, and imaging flow cytometry (IFCB)	1	1
Picoplankton & Bacteria	bio	Picoplankton and bacterioplankton abundances by flow cytometry	4	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	14	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	2	1
Genomics & eDNA	bio	Metabarcoding and environmental DNA — ASV tables, eDNA-derived abundance and density	0	0

Table 6.3: Every measurement type (200), 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	PHXXZZXX
dic_pco2_raw				Underway DIC raw pCO2
dic_ph_raw				Underway DIC raw pH
dic_salinity_psu		PSU		Underway DIC system salinity	PSLTZZ01
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
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
Meteorology & Sea State
barometric_pressure	yes	millibars		Barometric pressure	CAPHZZ01
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
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	EWDAZZ01
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	EWSBZZ01
Nutrients & Chemistry
ammonia	yes	umol/L	0 – 100	Ammonia concentration (QC'd)
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
isus_v	yes	V	-1 – 10	ISUS nitrate voltage
nitrate	yes	umol/L		Nitrate concentration	NTRAZZXX
nitrite	yes	umol/L	0 – 10	Nitrite concentration	NTRIZZXX
phosphate	yes	umol/L	0 – 10	Phosphate concentration	PHOSZZXX
silicate	yes	umol/L	0 – 300	Silicate concentration	SLCAZZXX
est_nitrate_cruise_corr		umol/L	0 – 200	Est. nitrate cruise-corrected
est_nitrate_sta_corr		umol/L	0 – 200	Est. nitrate station-corrected
r_ammonium		umol/L	0 – 100	Reported ammonium concentration (pre-QC)	AMONZZXX
Physical Oceanography
air_temp_c	yes	deg_C	-50 – 60	Air temperature	CTMPZZ01
atm_pressure_mb	yes	mb	800 – 1100	Atmospheric pressure (ship level)	CAPHZZ01
beam_attenuation	yes	1/m		Beam attenuation coefficient	ATTNXXZZ
bottom_depth_m	yes	m		Bottom depth (single-beam)	MBANZZ01
btl_depth	yes	m	0 – 11000	Bottle trip depth	ADEPZZ01
btl_temperature	yes	degC	-2 – 40	Bottle temperature	TEMPPR01
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
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_ml_l	yes	ml/L		Dissolved oxygen (QC'd)	DOXYZZXX
oxygen_ml_l_1	yes	ml/L	0 – 15	DO sensor 1 (uncorrected)	DOXYZZXX
oxygen_ml_l_2	yes	ml/L	0 – 15	DO sensor 2 (uncorrected)	DOXYZZXX
oxygen_ml_l_ave_sta_corr	yes	ml/L	0 – 15	DO average station-corrected	DOXYZZXX
oxygen_saturation	yes	%		Oxygen percent saturation	OXYSZZ01
oxygen_umol_kg	yes	umol/kg		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
rel_humidity_pct	yes	percent		Relative humidity	CRELZZ01
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_2	yes	PSU	0 – 45	Salinity sensor 2 (uncorrected)	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		Potential density (Sigma Theta)	SIGTEQ01
sigma_theta_1	yes	kg/m3	15 – 35	Potential density sensor 1	SIGTPR01
specific_volume_anomaly	yes	10^-8 m3/kg		Specific volume anomaly
sss_psu	yes	PSU	0 – 45	Sea surface salinity (raw)	PSLTZZ01
sst_c	yes	deg_C		Sea surface temperature (raw)	TEMPPR01
temperature	yes	degC		Water temperature (QC'd)	TEMPPR01
temperature_ave	yes	degC	-2 – 40	Average temperature	TEMPPR01
transmissometer	yes	%		Light transmissometer
tsg1_salinity_psu	yes	PSU		TSG unit 1 salinity	PSALSZ01
tsg1_temp_c	yes	deg_C	-2 – 40	TSG unit 1 temperature (physical sensor unconfirmed -- mets_03)	TEMPSZ01
uws_flow	yes	L/min		Underway seawater flow rate
wet_air_temp	yes	degC		Wet air temperature from sling psychrometer	CWETSS01
atm_pressure_slc_mb		mb		Atmospheric pressure (sea-level corrected)
bottom_depth		m		Water depth at the sampling event (sea floor depth beneath the cast)
bottom_depth_mb_m		m		Bottom depth (multibeam)	MBANZZ01
oxygen_ml_l_1_cruise_corr		ml/L		DO sensor 1 cruise-corrected	DOXYZZXX
oxygen_ml_l_1_sta_corr		ml/L		DO sensor 1 station-corrected	DOXYZZXX
oxygen_ml_l_2_cruise_corr		ml/L		DO sensor 2 cruise-corrected	DOXYZZXX
oxygen_ml_l_2_sta_corr		ml/L		DO sensor 2 station-corrected	DOXYZZXX
oxygen_sat_pct		percent	0 – 200	Dissolved oxygen saturation	OXYSZZ01
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		DO sensor 1 cruise-corrected	DOXMZZXX
oxygen_umol_kg_1_sta_corr		umol/kg		DO sensor 1 station-corrected	DOXMZZXX
oxygen_umol_kg_2_cruise_corr		umol/kg		DO sensor 2 cruise-corrected	DOXMZZXX
oxygen_umol_kg_2_sta_corr		umol/kg		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 (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)
salinity_1_corr		PSU	0 – 45	Salinity sensor 1 cruise-corrected	PSALST01
salinity_2_corr		PSU	0 – 45	Salinity sensor 2 cruise-corrected	PSALST02
sigma_theta_2		kg/m3	15 – 35	Potential density sensor 2	SIGTPR02
ss_conductivity		S/m	0 – 10	Sea surface conductivity (independent sensor)	CNDCZZ01
sss_psu_corrected		PSU	0 – 45	Corrected sea surface salinity	PSLTZZ01
sst_c_corrected		deg_C		Corrected sea surface temperature	TEMPPR01
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	CNDCSG01
tsg1_density		kg/m3		TSG unit 1 density
tsg1_salinity_psu_calibrated		PSU	0 – 45	Calibrated salinity	PSALSZ01
tsg1_sound_velocity		m/s		TSG unit 1 sound velocity	SVELXXXX
tsg1_temp_c_calibrated		deg_C	-2 – 40	Calibrated temperature	TEMPSZ01
tsg2_conductivity		S/m	0 – 10	TSG unit 2 conductivity	CNDCSG01
tsg2_density		kg/m3		TSG unit 2 density
tsg2_salinity_psu		PSU		TSG unit 2 salinity	PSALSZ01
tsg2_sound_velocity		m/s		TSG unit 2 sound velocity	SVELXXXX
tsg2_temp_c		deg_C		TSG unit 2 temperature (physical sensor unconfirmed -- mets_03)	TEMPSZ01
tsg2b_temp_c		deg_C	-2 – 40	A SECOND unit-2 temperature appearing alongside TSG_Temp_2 in one file	TEMPSZ01
tsg3_conductivity		S/m		TSG unit 3 conductivity	CNDCSG01
tsg3_density		kg/m3	900 – 1100	TSG unit 3 density
tsg3_salinity_psu		PSU	0 – 45	TSG unit 3 salinity	PSALSZ01
tsg3_sound_velocity		m/s		TSG unit 3 sound velocity	SVELXXXX
tsg3_temp_c		deg_C	-2 – 40	TSG unit 3 temperature (physical sensor unconfirmed -- mets_03)	TEMPSZ01
tsg5_salinity_psu		PSU	0 – 45	TSG unit 5 salinity	PSALSZ01
tsg5_temp_c		deg_C	-2 – 40	TSG unit 5 temperature (physical sensor unconfirmed -- mets_03)	TEMPSZ01
unknown_measurement_1				Unidentified measurement (NaN in every file inspected)
unknown_measurement_2				Unidentified measurement (NaN in every file inspected)
Phytoplankton
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)
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	0 – 100	Bottle chlorophyll-a	CPHLZZXX
btl_phaeopigment	yes	ug/L	0 – 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_fluor	yes	ug/L		Fluorescence (calibrated)	CPHLZZXX
chlorophyll_a	yes	ug/L		Chlorophyll-a measured fluorometrically	CPHLZZXX
fluorescence_v	yes	V	-1 – 15	Fluorescence voltage
light_pct	yes	%	0 – 100	Light intensity of incubation tubes
par	yes	uE/m2/s		Photosynthetically active radiation
par_surf	yes			Surface photosynthetically active radiation
phaeopigment	yes	ug/L		Phaeopigment measured fluorometrically	PHAEZZXX
spar	yes	uE/m2/s		Surface PAR
est_chlorophyll_a_cruise_corr		ug/L	0 – 1000	Est. chlorophyll-a cruise-corrected
est_chlorophyll_a_sta_corr		ug/L	0 – 1000	Est. chlorophyll-a station-corrected
pred_chl		ug/L		Estimated chlorophyll-a
Seabirds & Marine Mammals
behavior	yes			Seabird/marine-mammal behavior category (obs_attribute; e.g. Flying, Feeding)
count	yes	count	≥ 0	Organism count per survey transect
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.

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	6
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	4
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 v2026.09.06 — key, names, provider and category.

dataset_key	name	short name	provider	category	license
calcofi_bottle	CalCOFI Bottle Database	Hydrographic Bottle	calcofi	Physical Oceanography
calcofi_ctd-cast	CalCOFI CTD Cast Files	CTD Cast Files	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_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	custom
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.

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 and cdfw_dungeness-crab; 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, farallon, cufes.
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_bottle	123	123	flds_redefine.csv
calcofi_ctd-cast	6	5	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_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	26	6	flds_redefine.csv
swfsc_ichthyo	54	40	flds_redefine.csv

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_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_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_sample
cruise	cruise_orig		VARCHAR
stop_time	datetime_end_utc		TIMESTAMP
time	datetime_start_utc		TIMESTAMP
stop_latitude	latitude_stop		DOUBLE	decimal_degrees
stop_longitude	longitude_stop		DOUBLE	decimal_degrees
ship	ship_name		VARCHAR

swfsc_ichthyo

source name	standard name	source type	type	units
cruise
cruise_id	cruise_uuid	character	uuid
cruise_ymd	date_ym	numeric	date
ship	ship_key	character	varchar
egg
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
egg_stage
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
invert
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
larva
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
larva_size
len	length_mm	numeric	decimal	mm
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
larva_stage
netid	net_uuid	character	uuid
sppcode	species_id	numeric	smallint
net
netid	net_uuid	character	uuid
propsorted	prop_sorted	numeric	decimal	proportion
netside	side	character	varchar
shf	standard_haul_factor	numeric	decimal	dimensionless
towid	tow_uuid	character	uuid
volsampled	volume_sampled	numeric	decimal	m3
ship
shipcode	ship_key	character	varchar
shipname	ship_name	character	varchar
shipnodc	ship_nodc	character	varchar
site
cruise_id	cruise_uuid	character	uuid
latidude	latitude	numeric	decimal	decimal_degrees
orderocc	order_occ	numeric	smallint
stationid…1	site_uuid	character	uuid
stationid…7	station	numeric	decimal
species
tsn	itis_id	numeric	integer
taxon	scientific_name	character	varchar
sppcode	species_id	numeric	smallint
aphiaid	worms_id	numeric	integer
tow
starttime	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
code	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.