California Cooperative Oceanic Fisheries Investigations

Since 1949, hydrographic and biological data of the California Current System have been collected on CalCOFI cruises.  The 61 year hydrographic time-series includes temperature, salinity, oxygen and phosphate observations.  In 1961, nutrient analysis expanded to include silicate, nitrate and nitrite; in 1973, chlorophyll was added; in 1984, C14 primary productivity incubations were added.

These data are available on the CalCOFI website as:
 
IEH-Ascii Bottle Data (IEH-format) files (194903-201004), two versions (YY=year, MM=month):

• YYMMarch.ieh - observed data
• YYMMt.ieh - observed data with interpolated and/or CTD standard level data
• IEH Format Description - CalCOFI 128-column data archive, column-specific description.

CalCOFI Hydrographic Data are available as downloadable files in several formats (mdb, xml, csv, sql dump):

• 1949-2010 CalCOFI Hydrographic Data  Database (< click to download the Microsoft Access 2003 version; last update 1Sept2010; please note that this is a 'rar self-extracting exe', half the size of the previous zips) includes final hydrographic data from 1949-2010 (Apr 2010). All online versions of the database includes final, published data only. A research version with preliminary data is available by request from the CalCOFI data manager.
• CSV - 194903 to 201004 Cast & Bottle Tables as CSV (< click to download self-extracting rar exe, ver. 1Sept2010)
• XML - 194903 to 201004 Cast and Bottle XML files (1Sept2010; self-extracting rar exe) - Cast and Bottle tables as separate XML-XSD files
• SQL - 194903 to 201004 Access to MySQL 'dump' SQL file  (1Sept2010; self-extracting rar exe) - complete web version, includes Cast, Bottle, Cruise, Standard Station, Standard Depth, and metadata tables, uncompresses to over 870mb

Newest fixes and additions: 30 Aug  2010

• Added final data from CalCOFIs 1001NH & 1004MF.
• CalCOFI 0104JD station dates were off by -24hrs, fixed.
• Added missing stations 80.100 and 90.100 to 0911NH database.
• Please refer to Work_Done table in the database for additions, changes & corrections.
• Added content to Cruise_ID column: YYYY-MM-DD-Project Code-Ship Code
• Changed ShipName to Ship_Name in Cast table to match the 0-Ships table and establish a relational link
• Changed the Ship_Code to 4 characters only; UNOLS 2 digit country code + 2 char ship code
• Fixed 191001 glitch to 201001 in preliminary database

CTD data - 199308 - 201008 raw, preliminary-processed and bottle-corrected final 1m bin averaged Seabird 911+ temperature, salinity, oxygen, fluorometer, transmissometer, PAR, and ISUS electronic sensor data.

• CTD Query Form - 2009 Final Bottle-corrected CTD 1m binavg data search form; test page

Data reports (html or pdf from 1990 here). Hardcopy publications since 1953 are available in the UC library system.

• Data Report Format Description
• CalCOFI Reports - pdf versions are available online, hardcopies are available in
  the UC library system
• CalCOFI Atlases - index; hardcopies only available in the UC library system
• Zooplankton Collection - Datazoo's zooplankton online database information and query
• Data Summary - a few compiled papers for CalCOFI

The CalCOFI Hydrographic Database contains formatted IEH ascii data plus additional derived data published in the CalCOFI Hydrographic Data Reports. The legacy IEH format removes all decimal points and places data in specific columns. These data are re-formatted back into decimal form and imported into an Access database. Data column format & units are described in the IEH format description.

CalCOFI Hydrographic Data are available as downloadable files in several formats (mdb, xml, csv, sql dump):

• 1949-201004 CalCOFI Hydrographic Data Report Database (< click to download the Microsoft Access 2003 version; last update 1Sept2010; self-extracting rar exe) includes final hydrographic data from 1949-2010 (Apr 2010). All online versions of the database includes final, published data only. A research version with preliminary data is available by request from the CalCOFI data manager.
• CSV - 194903 to 201004 Cast & Bottle Tables as CSV (< click to download, ver. 1Sept2010 rar self-extracting exe)
• XML - 194903 to 201004 Cast and Bottle XML files (ver.1Sept2010 rar self-extracting exe) - Cast and Bottle tables as separate XML-XSD files
• SQL - 194903 to 201004 Access to MySQL 'dump' SQL file (ver. 1Sept2010) - complete web version, includes Cast, Bottle, Cruise, Standard Station, Standard Depth, and metadata tables, uncompresses to over 870mb

Newest fixes and additions:

1 Sept 2010

• Fixed date issue on 200104.  All dates were off by -24 hours.
• Added missing stations 80.0 100.0 and 90.0 100.0 to 200911.
• Added finalized data from cruises 201001 and 201004.

08 Jul 2010

• Please refer to the Work_Done table in the database for the latest corrections, changes, & additions.
• Added content to Cruise_ID column: YYYY-MM-DD-Project Code-Ship Code
• Changed ShipName to Ship_Name in Cast table to match the 0-Ships table and establish a relational link
• Changed the Ship_Code to 4 characters only; UNOLS 2 digit country code + 2 char ship code
• Fixed 191001 glitch to 201001 in preliminary database

18 Mar 2010

• Added Cruise_ID, YYYY-MM-DD-ProjectCode-ShipCode, column to cast table
• Changed the Ship_Code column which has historically been Country Code + Institution Code + Ship Code to Country Code + Ship Code because Institution is missing in most of the IEH archives.
• Revised the Ship Table: original two char ShipCode is now Ship, ShipCode is new standard country code+ship code
• Added 0911 final hydrographic data to the database

CTD Data are available in three main formats: zip-compressed raw cast files (.dat or .hex, .hdr, .con, .mrk, .bl Seasave data files); Seasave-processed .asc and .hdr (asciiout) down and up cast files; and combined data (1m depth binavg'd CTD .asc data merged with bottle data at ~20 depths) in csv-format.  The combined-data csvs include columns of 'Seasave-processed-only' 1m data and 'bottle vs CTD regression-corrected' 1m data. 

Latest asc-hdr data: 1008NH (Aug 2010 CalCOFI)

Latest bottle-corrected, combined data: 0911NM.

• CTD Query Form (Link Fixed 23Feb10) - prototype query form, search 2009 1m bottle-corrected CTD data. This form is subject to change, data presented are final bottle-corrected 1m binavg processed CTD. The complete CTD database (2009 - 0901, 0903, 0907) with metadata tables, correction coefficients, Seabird modules applied is available here. This is a new product and subject to change. Older CTD data will be re-processed to facilitate calibration coefficient import into the database (new software feature not applied to pre-2009 files)..
• CTD Data in all file formats via ftp: raw CTD data since 1992; asc CTD data since 2000; csv CTD+bottle data since 2008 (0801). To access the files using a ftp client, use the following settings:
  
  • host: ftp.iod.ucsd.edu
  • user: anonymous
  • password: user's email address
  • file path: /calcofi/CTD_Data/
  • port: 21 (do not use ssh or sftp)

DataZoo is a data repository and publishing system currently in use by multiple projects including the California Cooperative Oceanic Fisheries Investigation (CalCOFI) and two Long Term Ecological Research (LTER) sites, California Current Ecosystem (CCE), and Palmer (PAL). DataZoo provides a web-based interface to a database storing multidisciplinary data, metadata, and study information. This interface allows users to query the database and access data on a project, cruise, or dataset basis. (Information courtesy of the Oceaninformatics Group at SIO)

Since May 1987, bird and marine mammal observation census data have been collected on CalCOFI cruises during daylight transects between stations, weather-permitting.  Bird observers participating on CalCOFI are provided by support from the Farallon Institute (Jul 2007 to present) and Point Reyes Bird Observatory (PRBO, 1987-2006). Observation data can be found at Bird and Marine Mammal Observation Census Data at DataZoo.

CalCOFI Hydrographic Relational Database contains all IEH-ascii & Data Report data of the 60 year time-series. Microsoft Access version of the database (version 10292009) includes March 1949 to July 2009 bottle data plus recent CTD temperature and salinity data at bottle depths.

A queriable, abridged*, online version of the 1949-2009 database is available at latte.ucsd.edu. The search form will extract most hydrographic parameters such as temperature, salinity, oxygen, nutrients, and density vs time, depth, lat/lon. Biological parameters include chlorophyll and phaeopigments.
*primary productivity, weather, cruise, ship, and metadata tables are not included. Download the Access version for all data tables.

New(er) Beckman LS 6000IC (SysID# 231220) scintillation counter donated to SIO-CalCOFI by NOAA in early 2008.  Repaired by SIO-CalCOFI and in service Oct 2008,  replacing our broken/non-repairable Beckman LS 1801.

• First cruise counted on new counter: 0810NH
• New productivity import routine (DECODR, in-house data processing suite) written to ingest the new file format. Replicate 14C uptake calculations compared between old and new Beckman counters; agree within 95% CL.

4sec asc columns - for comparison to bottle data to derive correction coefficients
# name 0 = scan: Scan Count
# name 1 = timeJ: Julian Days; converted to DD MMM YYYY HH:MM:SS
# name 2 = prDM: Pressure, Digiquartz [db]
# name 3 = t090C: Temperature [ITS-90, deg C]
# name 4 = t190C: Temperature, 2 [ITS-90, deg C]
# name 5 = v0: Voltage 0
# name 6 = v1: Voltage 1
# name 7 = v2: Voltage 2
# name 8 = v3: Voltage 3
# name 9 = v4: Voltage 4
# name 10 = v5: Voltage 5
# name 11 = v6: Voltage 6
# name 12 = v7: Voltage 7
# name 13 = flSP: Fluorescence, Seapoint
# name 14 = latitude: Latitude [deg]
# name 15 = longitude: Longitude [deg]
# name 16 = depSM: Depth [salt water, m], lat = 33.2358
# name 17 = potemp090C: Potential Temperature [ITS-90, deg C]
# name 18 = potemp190C: Potential Temperature, 2 [ITS-90, deg C]
# name 19 = sal00: Salinity [PSU]
# name 20 = sal11: Salinity, 2 [PSU]
# name 21 = sigma-é00: Density [sigma-theta, Kg/m3]
# name 22 = sigma-é11: Density, 2 [sigma-theta, Kg/m3]
# name 23 = sbeox0ML/L: Oxygen, SBE 43 [ml/l], WS = 4
# name 24 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/Kg], WS = 4
# name 25 = sbeox0PS: Oxygen, SBE 43 [% saturation], WS = 4
# name 26 = dm: Dynamic Meters [10 J/Kg]
# name 27 = sva: Specific Volume Anomaly [10-8 * m3/Kg]


Final asc columns that are combined with corrected values & bottle data
# name 0 = scan: Scan Count
# name 1 = timeJ: Julian Days; converted to DD MMM YYYY HH:MM:SS
# name 2 = prDM: Pressure, Digiquartz [db]
# name 3 = t090C: Temperature [ITS-90, deg C]
# name 4 = t190C: Temperature, 2 [ITS-90, deg C]
# name 5 = v0: Voltage 0; relabeled to sensor voltage such as 'TransV'
# name 6 = v1: Voltage 1; relabeled to sensor voltage such as 'FluorV'
# name 7 = v2: Voltage 2; relabeled to sensor voltage such as 'AltV'
# name 8 = v3: Voltage 3; relabeled to sensor voltage such as 'PARV'
# name 9 = v4: Voltage 4; relabeled to sensor voltage such as 'O2V'
# name 10 = v5: Voltage 5; relabeled to specific sensor voltage if used
# name 11 = v6: Voltage 6; relabeled to sensor voltage such as 'ISUSV'
# name 12 = v7: Voltage 7; relabeled to specific sensor voltage if used
# name 13 = spar: SPAR/Surface Irradiance
# name 14 = bat: Beam Attenuation, Chelsea/Seatech/Wetlab CStar [1/m]
# name 15 = xmiss: Beam Transmission, Chelsea/Seatech/Wetlab CStar [%]
# name 16 = flSP: Fluorescence, Seapoint
# name 17 = latitude: Latitude [deg]
# name 18 = longitude: Longitude [deg]
# name 19 = depSM: Depth [salt water, m], lat = 34.39
# name 20 = potemp090C: Potential Temperature [ITS-90, deg C]
# name 21 = potemp190C: Potential Temperature, 2 [ITS-90, deg C]
# name 22 = sal00: Salinity [PSU]
# name 23 = sal11: Salinity, 2 [PSU]
# name 24 = sigma-é00: Density [sigma-theta, Kg/m3]
# name 25 = sigma-é11: Density, 2 [sigma-theta, Kg/m3]
# name 26 = sbeox0ML/L: Oxygen, SBE 43 [ml/l], WS = 4
# name 27 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/Kg], WS = 4
# name 28 = sbeox0PS: Oxygen, SBE 43 [% saturation], WS = 4
# name 29 = dm: Dynamic Meters [10 J/Kg]
# name 30 = sva: Specific Volume Anomaly [10-8 * m3/Kg]
# name 31 = nbin: number of scans per bin

Please note that sensor voltage column order may change from cruise to cruise; sensor type, units, brand or other specifics may vary; some sensor voltage columns may be missing when sensors are not installed.

Timeline of changes to data or methods

CTD asc filenames have typically been 'd or u' YYMMPPP.asc & .hdr (d or u = down or up casts; YY is year; MM month; PPP order occupied or proc #).  To standardize the file naming, the .asc & .hdr will be renamed to match the bottle-corrected csvs, YYYYMM_LLLLSSSS_PPPud.*, where YYMM is year month; LLLLSSSS is decimal Line & Sta (minus the '.'); PPP is order occupied (or processing number); u or d for up or down.