DOI: 10.5061/dryad.gf1vhhn0t
title: Alaska compendium of ocean profile data [ACOD]: Archival CTD and nutrient hydrography from NOAA's EcoFOCI, EMA, and predecessor programs

description: This oceanographic data product represents a multi-decade collection of
 shipboard hydrography in Alaska waters, sampled by select programs of the
 US National Oceanic and Atmospheric Administration (NOAA).  Data
 types include basic physical (temperature and salinity) and chemical
 (dissolved nutrient) properties collected as profiles from oceanographic
 research vessels.  The geographic extent includes coastal and
 offshore areas of the Gulf of Alaska, Bering Sea, and the Chukchi
 Sea.  Temporal coverage is 1974-2021 (temperature and salinity)
 or 2001-2021 (nutrient data).  Data in this product were
 collected under programs associated with the NOAA Pacific Marine
 Environmental Laboratory (PMEL) and Alaska Fisheries Science Center
 (AFSC).  Three major data collection efforts are represented: (1)
 the Ecosystems and Fisheries-Oceanography Coordinated Investigations
 (EcoFOCI) program (PMEL and AFSC); (2) the Ecosystem Monitoring and
 Assessment program led by AFSC and supported by EcoFOCI; and (3)
 historical data collected between the founding of PMEL in 1973 and the
 beginning of EcoFOCI in 1984.  Data were pooled across cruises
 and years into a concatenated, single-point-of-access product, with
 additional quality control applied to cruise records, profile data, and
 nutrient data.  Simple derived quantities and indexing are
 included for ease of use.  The data product is fully described in
 Mordy et al. (2025, "A compendium of temperature and salinity
 profiles and discrete nutrients from selected NOAA programs in
 Alaska," Scientific Data).
description: Sampling methods and instrumentation have varied across years and
 sources.  Temperature and salinity profiles (1974-2021) were collected
 using profiling Conductivity and Temperature with Depth (CTD)
 instruments.  Early CTD data quality in highly stratified waters was often
 compromised due to rapid profiling through a sharp thermocline; salinity
 data prior to April 1987 are of lower quality in some cruises and should
 be used with care.  Since approximately 1988, the sampling instrument of
 choice has been the SeaBird Electronics (SBE) 911plus system.  On some
 earlier EMA cruises (prior to 2018), an SBE25 was used.  Sampling during
 the EcoFOCI program involved standardized descent rates that increase with
 depth, filtering and binning to standard 1 dbar resolution, additional
 post-processing to ensure data integrity, and consistent rules for surface
 interpolation.  Salinity was reported in units of parts per thousand prior
 to August 1995 and PSS-78 thereafter.  Dissolved inorganic nutrient data
 (2001-2021; phosphate, silicic acid, nitrate, nitrite, and ammonium) were
 sampled by PMEL/EcoFOCI or EMA.  Samples were collected at discrete depths
 from Niskin bottles attached to the CTD rosette and were measured using
 autoanalyzers with segmented flow.  Samples were processed by PMEL or at
 the University of Washington Marine Chemistry Laboratory for EMA data
 2003-2011.  Protocols utilized at all locations were comparable and
 included calibration of labware, preparation of primary and secondary
 standards, and corrections for blanks, refractive index and carryover.
 Ammonium was analyzed on most, but not all cruises.
description: **Dataset Overview** This product represents a single-point-of-access,
 quality-controlled collection of basic shipboard hydrographic data
 (temperature, salinity, and nutrients). These were sampled by select
 programs of the US National Oceanic and Atmospheric Administration (NOAA)
 in Alaska waters, including the Gulf of Alaska (GOA), Bering Sea (BS), and
 Chukchi Sea (CS). Data coverage is 1974-2021 (CTD) or 2001-2021
 (nutrient). Data sources and methodology are fully described in Mordy et
 al. (2025, "A compendium of temperature and salinity profiles and
 discrete nutrients from selected NOAA programs in Alaska",
 *Scientific Data*) and are briefly summarized here. NOAA's Pacific
 Marine Environmental Laboratory (PMEL) was established in 1973, and
 thereafter began environmental studies in Alaska waters that focused on
 the physical dynamics of the GOA, eastern BS, and CS. In 1984 a new
 program was established between PMEL and NOAA's Alaska Fisheries
 Science Center (AFSC) now known as Ecosystems and Fisheries-Oceanography
 Coordinated Investigations (EcoFOCI). This program was initially focused
 on the Gulf of Alaska relating to the walleye pollock fishery and then
 expanded into the Bering Sea and to other fish species, with subsequent
 expansion into the Chukchi Sea. Long-term mooring sites were established
 and maintained, along with repeated hydrographic and biological surveys to
 monitor the seasonal and interannual dynamics of these ecosystems. In
 1999, the AFSC Environmental Monitoring and Assessment program (EMA)
 program began to survey fish populations over the southeastern BS, as part
 of the Bering-Aleutian Salmon International Survey (BASIS); these gridded
 surveys were later extended to the northern BS and CS. This data
 compendium integrates archival oceanographic sampling from all of these
 sources. The goals of this compendium dataset were to concatenate these
 sources into a single product, assess data quality and provide additional
 quality control measures, along with simple derived variables for ease of
 use. Temperature and salinity profiles have been reviewed and vetted for
 outliers. Archival cast location and time were screened based on the
 implied minimum vessel speed between profiles and corrected where possible
 based on digitized cruise logs. Reported bottom depth data were screened
 for agreement with sampling depth and corrected where possible. A version
 of salinity with suspect portions of profiles automatically deleted was
 constructed and included alongside archival data. Derived variables were
 estimated to augment the nutrient dataset, including dissolved inorganic
 nitrogen, and variables intended to help quickly identify whether samples
 are located in the surface mixed layer. These procedures and their results
 are described fully in Mordy et al. (2025). This product complements the
 archiving of individual cruise data at the National Centers for
 Environmental Information and other repositories; cross-reference
 information and links to these repositories are included where available.
 **File Description** The product assembles data from multiple cruises and
 years into five files. CTD data are contained in two netCDF files, which
 differ in the maximum depth extent that is included. Nutrient data are
 presented identically in two formats (netCDF and comma-separated-values).
 The fifth file includes cruise summary data. **The five data files:** *
 (1) ACOD_CTD_v1.0.nc\ A netCDF-4 file containing temperature and salinity
 profile data and metadata. CTD data are stored as 2-dimensional arrays of
 profiles versus pressure and time. * (2) ACOD_CTD-250_v1.0.nc\ Identical
 to (1), but truncated to include only the top 250 dbar of data. * (3)
 ACOD_NUT_v1.0.nc\ A netCDF-4 file containing nutrient data at discrete
 depths along with temperature and salinity from item (1), metadata, some
 derived quantities (e.g., total dissolved inorganic nitrogen [DIN]), and
 quality flags. Nutrient data are stored as 1-dimensional columns for each
 variable. * (4) ACOD_NUT_v1.0.csv\ A version of (3) that is stored in a
 comma-separated-values format. * (5) ACOD_CRUISE_v1.0.csv\ A
 comma-separated-values table containing cruise summary metadata. The
 vertical coordinate for the data is pressure in units of dbar. Other
 collected or sampled variable types exist in some of the original data
 sets but have been excluded from this data product. NetCDF files in this
 data product adhere to the [Climate and Forecast (CF) Metadata
 Conventions, version
 1.8](https://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html). Missing data are indicated by 1.0e35 in netCDF files, and NA in the nutrient csv file (4). All flags follow WOCE flagging conventions ([Swift, 2008](https://cchdo.github.io/hdo-assets/documentation/policies/CCHDO_DataSubmitGuide.pdf)); 2=acceptable measurement, 3=questionable measurement, 4=bad measurement, 5=not reported. **Salinity Quality Control Variables** In (1)-(2), salinity variables appended with "_with_QC_applied" have suspect salinity regions deleted. Portions of profiles to be deleted were identified using an automated procedure, locating errors sufficient to cause a statically unstable profile (negative square buoyancy frequency N^2^) that exceeds a set threshold (N^2^ &lt; -1x10^-4^ s^-2^). This process is described fully in Mordy et al. (2025). Salinity data prior to April 1987, stored in the variables "Salinity_PPT" or "Salinity_PPT_with_QC_applied", are of lower quality in some cruises and should be inspected prior to use. **Detailed File Contents/Variables** **CTD Files (1)-(2)** **PROFILE** - arbitrary full-dataset profile number (1 to 27917), used to index profiles. \ **TIME** - profile time in days since 1900-01-01.\ **LONGITUDE** - profile longitude in degrees east.\ **LATITUDE** - profile latitude in degrees north.\ **BOTTOM_DEPTH** - bottom depth in meters as recorded in original cruise records. This variable is populated where available but missing in some instances.\ **REGION** - profile geographic region (Gulf of Alaska, Bering Sea, Chukchi Sea).\ **CRUISE_NUMBER** - arbitrary full-dataset cruise number for each profile. Cruise numbers can be cross-referenced to ACOD_CRUISE_v1.0.csv.\ **CRUISE_NAME** - cruise name for each profile.\ **CAST** - cast number within each cruise.\ **PRESSURE** - pressure grid (dbar) on which profile data are stored.\ **Temperature** - profile temperature (degrees C) in a 2-d array of dimensions [PROFILE] x [PRESSURE].\ **Salinity_PPT** - profile salinity in a 2-d array of dimensions [PROFILE] x [PRESSURE]. This variable stores data from older cruises (pre-August 1995) reporting data in units of "Parts Per Thousand".\ **Salinity_PPT_with_QC_applied** - same data as in variable "Salinity_PPT", but with suspect regions deleted as described above.\ **Salinity_PSS** - profile salinity in a 2-d array of dimensions [PROFILE] x [PRESSURE]. This variable stores data from newer cruises (August 1995-on) reporting Practical Salinity.\ **Salinity_PSS_with_QC_applied** - same data as in variable "Salinity_PSS", but with suspect regions deleted as described above. **Nutrient Files (3)-(4)** **SAMPLE** - arbitrary full-dataset sample number (1 to 45357) used to index nutrient samples, present in file (3) only (NetCDF file).\ **CRUISE_NUMBER** - arbitrary full-dataset cruise number for sample profile. Cruise numbers can be cross-referenced to ACOD_CRUISE_v1.0.csv.\ **CRUISE_NAME** - cruise name for sample profile.\ **CAST** - sample profile cast number within each cruise.\ **BOTTLE_NUMBER** - Niskin sample number within a profile. This variable is populated where available but missing in some instances.\ **PRESSURE** - nutrient sample pressure (dbar).\ **TIME** - sample profile time in days since 1900-01-01.\ **LONGITUDE** - sample profile longitude in degrees east.\ **LATITUDE** - sample profile latitude in degrees north.\ **BOTTOM_DEPTH**- sample profile bottom depth in meters as recorded in original cruise records. This variable is populated where available but missing in some instances.\ **REGION** - sample profile geographic region (Gulf of Alaska, Bering Sea, Chukchi Sea).\ **NO3** - nitrate concentration in micromoles per liter.\ **NO3_QC** - status/quality flag for nitrate concentration. As noted above, flags follow WOCE flagging conventions ([Swift, 2008](https://cchdo.github.io/hdo-assets/documentation/policies/CCHDO_DataSubmitGuide.pdf)); 2=acceptable measurement, 3=questionable measurement, 4=bad measurement, 5=not reported. For Ocean Data View (ODV) users working with the .csv file (4), manually renaming a flag variable as, e.g. for NO3, "NO3_FLAG_W", will allow ODV to easily link the quality control flag with the parameter of interest.\ **NO2** - nitrite concentration in micromoles per liter.\ **NO2_QC** - status/quality flag for nitrite concentration.\ **NH4** - ammonium concentration in micromoles per liter.\ **NH4_QC** - status/quality flag for ammonium concentration.\ **PO4** - phosphate concentration in micromoles per liter.\ **PO4_QC** - status/quality flag for phosphate concentration.\ **H4SiO4** - orthosilicic acid concentration in micromoles per liter.\ **H4SiO4_QC** - status/quality flag for orthosilicic acid concentration.\ **DIN** - sample dissolved inorganic nitrogen (DIN) concentration in micromoles per liter. DIN is calculated as the sum of NO3, NO2, and NH4 variables; where any of these variables is missing, DIN is also missing.\ **DIN_QC** - status/quality flag for DIN concentration.\ **DIN0** - alternate sample dissolved inorganic nitrogen (DIN0) concentration in micromoles per liter. DIN0 is calculated as for DIN (NO3+NO2+NH4), but if either NO2 or NH4 is missing, these concentrations are assumed to be zero. However, if NO3 is missing, DIN0 is also missing.\ **DIN0_QC** - status/quality flag for DIN0 concentration.\ **NUT_COMMENT** - comments/notes on sample characteristics, where applicable.\ **Temperature** - CTD profile temperature (degrees C) interpolated to sample bottle depth.\ **Salinity** - CTD profile Practical Salinity (PSS-78) interpolated to sample bottle depth, using the "Salinity_PSS_with_QC_applied" variable from (1)-(2). Nutrient data are reported starting in 2001, after the transition of salinity from PPT to Practical Salinity.\ **MLD10** - sample profile mixed-layer depth (dbar) from 10 dbar reference, based on 0.03 kg m^-3^ density increment.\ **ILD10** - sample profile isothermal-layer depth (dbar) from 10 dbar reference, based on 0.2 degrees C temperature increment of either sign.\ **Delta_Sig10** - difference in density (sigma-t, kg m^-3^) between sample depth and 10 dbar reference, in sample profile.\ **Delta_T10** - difference in temperature (degrees C) between sample depth and 10 dbar reference, in sample profile.\ **Cruise Table (5)** **CRUISE_NUMBER** - arbitrary full-dataset cruise number, referenced in CTD and nutrient files.\ **CRUISE_NAME** - cruise name as assigned in EcoFOCI/EMA records.\ **VESSEL** - research vessel used for cruise.\ **Number_of_Casts** - number of casts from each cruise included in the data product.\ **Total_Nutrient_Samples** - number of rows in the nutrient data product files that correspond to this cruise.\ **First_Cast** - date of first cast included in the data product.\ **Last_Cast** - date of last cast included in the data product.\ **Min_Latitude_degN**, **Max_Latitude_degN**, **Min_Longitude_degE**, **Max_Longitude_degE** - lat/lon coordinates of bounding box containing all casts from this cruise in the data product.\ **SalQC_Proportion_of_Casts_Applied** - the proportion of casts in a cruise in which any data were deleted, located in the "Salinity_*_with_QC_applied" salinity variables.\ **SalQC_Mean_Vertical_Extent_dbar** - in casts where salinity data were deleted, the average vertical extent deleted.\ **SalQC_Mean_Extent_Still_Unstable_dbar** - in all casts, the average vertical extent of data remaining below a lower threshold for instability [N^2^ &lt; -1x10^-5^ s^-2^], after QC application to salinity profiles.\ **Accession** - where available, NCEI accession number(s) for repository data associated with this cruise.\ **Program** - where available, NOAA program or project that was the subject of this cruise. Acronyms used in the Program field are listed below.\ **Link** - where available, link to any lower-level archival data associated with this cruise, which may include other variable types not part of the ACOD product.\ **Region** - geographic region(s) covered by this cruise (GOA: Gulf of Alaska, BS: Bering Sea, CS: Chukchi Sea). **Program Field Acronyms**\ AFSC: NOAA Alaska Fisheries Science Center\ AOOS: Alaska Ocean Observing System\ Arctic EIS: Arctic Ecosystem Integrated Survey\ ARCWEST: Arctic Whale Ecology Study\ ARI: NOAA Arctic Research Initiative\ BASIS: Bering Arctic Subarctic Integrated Survey\ BEST: Bering Sea Ecosystem Study\ BOEM: Bureau of Ocean Energy Management\ BOEMRE: Bureau of Ocean Energy Management, Regulation, and Enforcement\ BSIERP: Bering Sea Integrated Ecosystem Research Program\ CHAOZ: CHukchi Acoustic, Oceanographic, and Zooplankton\ EcoFOCI: Ecosystem and Fisheries Oceanography Coordinated Investigations\ EMA: NOAA AFSC Ecosystem Monitoring, and Assessment\ FOCI: Fisheries Oceanography Coordinated Investigations\ GLOBEC: Global Ocean Ecosystem Dynamics\ GOAIERP: Gulf of Alaska Integrated Ecosystem Research Program\ GOAIERP-LTL: Gulf of Alaska Integrated Ecosystem Research Program-Lower Trophic Level\ GOAIERP-UTL: Gulf of Alaska Integrated Ecosystem Research Program-Upper Trophic Level\ IARC: International Arctic Research Center\ IGOSS: Integrated Global Ocean Service System\ IMS-UAF: Institute of Marine Sciences, University of Alaska-Fairbanks\ MACE: AFSC Midwater Assessment and Conservation Engineering Program\ MIZEX: Marginal Ice Zone Experiment\ NMFS: National Marine Fisheries Service\ NMML: National Marine Mammal Laboratory\ NOS: National Ocean Service\ NPCREP: North Pacific Climate Regimes and Ecosystem Productivity\ NPMR, NPMRP: North Pacific Marine Research\ NPRB: North Pacific Research Board\ NSF: National Science Foundation\ OCC: Ocean Carrying Capacity (GLOBEC)\ OCSEAP: Outer Continental Shelf Environmental Assessment Program\ OER: NOAA Office of Ocean Exploration and Research\ PacTOP: Pacific Tsunami Observational Program\ PMEL: Pacific Marine Environmental Laboratory\ RACE: AFSC Resource Assessment and Conservation Engineering Program\ RUSALCA: Russian-American Long-Term Census of the Arctic\ SEBS: Southeast Bering Sea\ SEBSCC: Southeast Bering Sea Carrying Capacity\ SECM: Southeast Coastal Monitoring\ SSL: Steller Sea Lion\ TAO: NOAA Tropical Atmosphere Ocean Array\ UAF: University of Alaska Fairbanks **Usage Notes** These data are free for public use under the [CC0 1.0 license](https://creativecommons.org/public-domain/cc0/). If you use or publish these data we request that you cite both the data set (DOI: 10.5061/dryad.gf1vhhn0t) and the data description article (Mordy et al, 2025). Additionally, please notify authors herein of any related publications.