California Cooperative Oceanic Fisheries Investigations

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 1949, hydrographic and biological data of the California Current System have been collected on CalCOFI cruises.  The 60+ 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:

• 1949-2009 CalCOFI Hydrographic Data Query Form (http://db.calcofi.net/index.html) - search 60 years of time-series data by entering specific criteria such as date-time, CalCOFI Line and/or Station, cruise, and depth. Query results display in tabular form in your web browser and may be exported (downloaded) in doc, csv, xls, & xml formats. This online version of cast & bottle data have been combined into a single database table to make queries a single operation. Some data columns are not yet queriable online (primary productivity depth data, for example) but all data presented are published, final data. For a complete version of the hydrographic database, download the MS Access database or Sql versions listed below. For integrated data queries such as ichthyoplankton + hydrographic data, try DataZoo.
• Database - Mar 1949 - Jul 2009 (ver 17Dec09: CalCOFI_Bottle_Data_1949-200907.zip) hydrographic bottle data report (IEH data + published Data Report data); Microsoft Access format
  • Csv - (CalCOFI_Bottle_Data_1949-200907_csvs.zip; updated 17 Dec 2009) bottle and station information csvs used to create the Access database. Seabird-software processed CTD 1m binavg data combined with and corrected by bottle data in comma-separated-values format.
  • Sql - (calcofi_iehdata_194903-200907SQL.zip) a sql dump of the web version of the database (from phpadmin/mysql).

• Downloadable Bottle (IEH-format) ascii files (1949-2009). two versions: (YY=year, MM=month)

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

• Queriable, abridged*, online version of the 1949-2009 database is available at db.calcofi.net. This is a developmental page and subject to change but all data extracted are from the published CalCOFI Data Reports and final data database. The search form will extract core hydrographic parameters such as temperature, salinity, oxygen, nutrients, and density vs depth, time, lat/lon. Biological parameters include chlorophyll and phaeopigments. The search results will display in tabular form and may be exported-downloaded as doc,xls, csv, & xml files.
  *primary productivity depth data, weather, cruise, ship, and metadata tables are not yet queriable online. Download the database files(s) for all data tables or visit DataZoo's online query page.
  
• 1949-2009 CalCOFI Hydrographic Data Report Database (< click to download the Microsoft Access 2003 version; last update 17Dec2009) includes final hydrographic data from 1949-2009 (0907). 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.
• CSVs - 1949-2009 Database Cast & Bottle Tables as csvs (< click to download, ver. 17Dec2009)
• XML - 194903 to 200907 Combined Cast+Bottle XML file - uncompresses to over 700mb
• XML - 194903 to 200907 Cast and Bottle XML files - Cast and Bottle tables as separate XML files
• SQL - 194903 to 200907 Access to MySQL 'dump' SQL file - complete web version, includes Cast, Bottle, Cruise, Standard Station, Standard Depth, and metadata tables, uncompresses to over 870mb

Since 1949, hydrographic and biological data of the California Current System have been collected on CalCOFI cruises.  The 60+ year hydrographic time-series includes temperature, salinity, oxygen and phosphate observations.  In 1961, nutrient analyses added silicate, nitrate and nitrite; in 1973, chlorophyll and phaeopigments were added; in 1984, C14 primary productivity incubations were added.
These data are available on the CalCOFI or DataZoo website as:

• 1949-2009 CalCOFI Hydrographic Data Query Form (http://db.calcofi.net/index.html) - search 60+ years of time-series data by entering specific criteria such as date-time, CalCOFI Line and/or Station, cruise, and depth. Query results display in tabular form in your web browser and may be exported (downloaded) in doc, csv, xls, & xml formats. This online version of cast & bottle data have been combined into a single database table to make queries a single operation. Some data columns are not yet queriable online (primary productivity depth data, for example) but all data presented are published, final data. For a complete version of the hydrographic database, download the MS Access database or Sql versions listed below. For integrated data queries such as ichthyoplankton + hydrographic data, try DataZoo.
• Database - Mar 1949 - Jul 2009 (ver 17Dec09: CalCOFI_Bottle_Data_1949-200907.zip) hydrographic bottle data report (IEH data + published Data Report data); Microsoft Access format
  • Csv - (CalCOFI_Bottle_Data_1949-200907_csvs.zip; updated 17 Dec 2009) bottle and station information csvs used to create the Access database. Seabird-software processed CTD 1m binavg data combined with and corrected by bottle data in comma-separated-values format.
  • Sql - (calcofi_iehdata_194903-200907SQL.zip) a sql dump of the web version of the database (from phpadmin/mysql).
• Hydrographic and integrated data query form via DataZoo
• Downloadable IEH ascii files (1949-2009). two versions: (YY=year, MM=month)
  • observed data (YYMMarch.ieh)
  • observed data with interpolated standard levels (YYMMt.ieh)
• IEH Format Description - CalCOFI 128-column data archive, column-specific description.
• Data reports (html or pdf from 1990 here). Hardcopy publications since 1953 are available in the UC library system
  
  • Data Report Format Description

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: 0903JD (Mar 2009 CalCOFI); latest bottle-corrected, combined data: 0801JD.

• CTD Data in all formats via ftp: raw CTD data since 1992; asc CTD data since 2000; csv CTD+bottle data since 2006

• Bird and Marine Mammal Observation Census Data at DataZoo

 

• 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.