CalCOFI Data - Database Definitions

Database Definitions

Table and Column Definitions of the CalCOFI Database:

Station_ID Table	(Station ID & Desired Position Information)
ID	Autonumbered	Long Integer
Sta_ID	LineSta	Text
Line	CalCOFI Line	Text
Sta	CalCOFI Station	Integer
DLat_Dec	Desired Position Decimal Latitude	Single
DLat_Deg	Desired Position Lat Degrees	Integer
DLat_Min	Desired Position Lat Minutes	Single
DLat_Hem	Desired Position Lat Hemisphere	Text
DLon_Dec	Desired Position Decimal Longitude	Single
DLon_Deg	Desired Position Lon Degrees	Integer
DLon_Min	Desired Position Lon Minutes	Single
DLon_Hem	Desired Position Lon Hemisphere	Text
Stnd_Sta	ST denotes current standard station	Text

Cast_Data Table	(Station Cast Observed Information)
Cst_Cnt	Autonumbered - 1 is first sta done	Long Integer
Sta_ID	See Description	Text
Cast_ID	See Description	Text
Quarter	1, 2, 3, or 4	Integer
Date	Cast Date UTC	Date/Time
Year	Cast Year UTC	Integer
Month	Cast Month UTC	Integer
Julian_Day	Cast Julian Day UTC (1=Jan 1)	Integer
Time	Cast Time UTC	Date/Time
Lat_Dec	Observed Latitude Decimal Degrees	Single
Lat_Deg	Observed Latitude Degrees	Integer
Lat_Min	Observed Latitude Minutes	Single
Lat_Hem	Observed Latitude Hemisphere	Text
Lon_Dec	Observed Longitude Decimal Degrees	Single
Lon_Deg	Observed Longitude Degrees	Integer
Lon_Min	Observed Longitude Minutes	Single
Lon_Hem	Observed Longitude Hemisphere	Text
Line	IEH-Reported Line	Text
StndL	Nearest Standard Line	Integer
CalcLine	Calculated Line	Integer
Sta	IEH-Reported Station	Integer
StndS	Nearest Standard Station	Integer
CalcSta	Calculated Station	Integer
Bottom_D	Bottom Depth meters	Integer
ShipName	Ship's Name	Text
Ship_Code	Ship's NODC Code	Text
Data_Type	See Description	Text
Orig_Sta_ID	IEH-Reported Station ID	Text
Cruz_Num	YYMM Cruise Designation	Text
IntChl	Integrated Chlorophyll	Single

Bottle_Data Table	(Hydrographic Bottle Data)
Cst_Cnt	Autonumbered Cast Count	Long Integer
Btl_Cnt	Autonumbered Bottle Count	Long Integer
Sta_ID	See Description	Text
Depth_ID	See Description	Text
Depthm	Bottle Depth meters	Integer
T_degC	Temperature degrees C	Single
Salnty	Salinity	Single
O2ml_L	Oxygen ml/L	Single
STheta	Density as sigma-theta	Single
O2Sat	Oxygen Saturation %	Single
RecInd	Record Indicator	Integer

Nutrient_Data Table	(Bottle Nutrient Data)
Btl_Cnt	Autonumbered Bottle Count	Long Integer
PO4ug	Phosphate uM/L	Single
PO4q	Phosphate quality	Integer
SiO3ug	Silicate uM/L	Single
SiO3q	Silicate quality	Integer
NO2ug	Nitrite uM/L	Single
NO2q	Nitrite quality	Integer
NO3ug	Nitrate uM/L	Single
NO3q	Nitrate quality	Integer

Chla_Data Table	(Chlorophyll Data)
Btl_Cnt	Autonumbered Bottle Count	Long Integer
ChlorA	Chlorophyll-a ug/L	Single
Chlqua	Chlorophyll-a quality	Integer
Phaeop	Phaeopigments ug/L	Single
Phaqua	Phaeopigments quality	Integer

Bottle_Qual Table	(Bottle Data Precision-Quality Codes)
Btl_Cnt	Autonumbered Bottle Count	Long Integer
T_prec	Temperature precision	Integer
T_qual	Temperature quality	Integer
S_prec	Salinity precision	Integer
S_qual	Salinity quality	Integer
O_qual	Oxygen precision	Integer
SThtaq	Sigma-theta quality	Integer
O2Satq	Oxygen saturation quality	Integer

Prodo_Cast Table	(Primary Productivity Cast Info)
Cst_Cnt	Autonumbered Cast Count	Long Integer
Cast_ID	See Description	Text
Inc_Str	Incubation Start Time PST	Date/Time
Inc_End	Incubation End Time PST	Date/Time
PST_LAN	Local Apparent Noon PST	Text
Civil_T	Civil Twilight PST	Date/Time
TimeZone	Timezone (+8)	Text
IntC14	Integrated C14 Assimilation	Single

Prodo_Data Table	(Primary Productivity-C14 Uptake)
Cst_Cnt	Autonumbered Cast Count	Long Integer
Btl_Cnt	Autonumbered Bottle Count	Long Integer
C14As1	C14 Assimilation Sample 1	Single
C14A1p	C14 Assimilation Sample 1 precision	Integer
C14A1q	C14 Assimilation Sample 1 quality	Integer
C14As2	C14 Assimilation Sample 2	Single
C14A2p	C14 Assimilation Sample 2 precision	Integer
C14A2q	C14 Assimilation Sample 2 quality	Integer
DarkAs	C14 Assimilation Dark Sample	Single
DarkAp	C14 Assimilation Dark Samp precision	Integer
DarkAq	C14 Assimilation Dark Samp quality	Integer
MeanAs	C14 Mean Assimilation	Single
MeanAp	C14 Mean Assimilation precision	Integer
MeanAq	C14 Mean Assimilation quality	Integer
IncTim	Incubation Time	Date/Time
LightP	Light Level-Percentage	Single

Weather_Data Table	(uses WMO Weather Codes)
Cst_Cnt	Autonumbered - 1 is first sta done	Long Integer
Wave_Dir	Wave Direction Code	Integer
Wave_Ht	Wave Height Code	Integer
Wave_Prd	Wave Period Code	Integer
Wind_Dir	Wind Direction Code	Integer
Wind_Spd	Wind Speed Code	Integer
Barometer	Barometric pressure	Single
Dry_T	Dry Temperature	Single
Wet_T	Wet Temperature	Single
Wea	Weather Code	Integer
Cloud_Typ	Cloud Type Code	Integer
Cloud_Amt	Cloud Amount Code	Integer
Visibility	Visibility Code	Integer
Secchi	Secchi Depth	Integer
ForelU	Forel Color Scale	Integer

Rpt_Data Table	(CalCOFI Data Report Data)
Btl_Cnt	Autonumbered Bottle Count	Long Integer
R_Depth	Reported Depth meters	Integer
R_TEMP	Reported Temperature deg C	Single
R_POTEMP	Reported Potential Temperature	Single
R_SALINITY	Salinity	Single
R_SIGMA	Sigma-theta	Single
R_SVA	Specific Volume Anomaly	Single
R_DYNHT	Dynamic Height	Single
R_O2	Oxygen ml/L	Single
R_O2Sat	Oxygen Saturation %	Single
R_SIO3	Silicate	Single
R_PO4	Phosphate	Single
R_NO3	Nitrate	Single
R_NO2	Nitrite	Single
R_CHLA	Chlorophyll-a	Single
R_PHAEO	Phaeopigments	Single
R_PRES	Pressure db	Integer
R_SAMP	Sample number	Integer

Cruise Hydrographic Data Reports

We report the data that we collect on our cruises in a Hydrographic Data Report. These reports consist of:

Introductions - Contains the standard procedures, tabulated data descriptions, associated ancillary projects, footnote definitions, and literature cited.

Hydrographic Data Reports - Quarterly tabulated data reports. The 60 year dataset includes temperature, salinity, oxygen and phosphate observations. In 1961, nutrient analysis expanded to include silicate, nitrate and nitrite; in 1973, chlorophyll was added; in 2008, the nutrient analysis expanded to include ammonium.

Primary Productivity Data Reports - Quarterly Tabulated Data Reports. These are a subset of the hydrographic data report containing only stations in which primary productivity experiments were carried out. Includes hydrographic data along with primary productivity data.

Personnel - List of personnel per cruise, cruise dates, ports of call, ship name, and captain's name.

Macrozooplankton Biomass Report - Contains the macrozooplankton biomass, as wet displacement volume, after removal of large (>5 ml) organisms from the starbird side of a 71 cm mouth diameter paired net (bongo net) equipped with 0.505mm plankton mesh; towed obliquely from 210 meters to the surface.

Spatial Pattern Figures - Contains vertical (line 90 only) and horizontal (10 and 200 meters along the standard CalCOFI grid) contour plotted hydrographic data.

Bird Figures - Quartely Avifauna distribution observations over the standard CalCOFI grid.

For combined quarterly CalCOFI Data Reports in pdf, please see our CalCOFI Data Reports web page.

Microsoft Access Database

Microsoft Access Database (mirror) - March 1949 - April 2010 hydrographic bottle data (IEH data + published Data Report data); Microsoft Access format (version 1Sept2010). Table and Column Definitions of the CalCOFI Database.

XML - 194903 to 201004 Cast and Bottle XML files (mirror) - Cast and Bottle tables as separate XML files.

SQL - 194903 to 2001004 Access to MySQL 'dump' SQL file (mirror)- 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 -1 day off
Added missing stations 80.0 100.0 and 90.0 100.0 to 200911
Added finalized data from cruises 201001 and 201004

23 Mar 2010

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

17 Dec 2009

Salinity decimal accuracy set to 3 sig figs
Sigma-theta decimal accuracy set to 3 sig figs
Cast_ID Julian Day, Time, Data_Type corrected on several casts
Depth_ID corrected to match Cast_ID corrections
Prodo_Cast table - removed Cast_ID, not needed since Cast_Cnt relation links Cast table Cast_ID

07 Dec 2009

Cruise 198107 changed to 198108 as reported by NMFS ichthyoplankton database
Cruise 199007 changed to 199008 as reported by NMFS ichthyoplankton database
Shipcode edit; removed two spaces between country code and ship code

18 November 2009

Decimal Latitude and Longitude decimal values recalculated to 5 decimal places from Lat_Deg+(Lat_Min/60) and Lon_Deg+(Lon_Min/60).
Updated online versions of database & csvs with recalculated lat & lon columns
Added xml and mysql dump download links.

21 October 2009

Cast_ID column in the Cast Table has been synchronized with the Ship_Code column from the Cast Table. Depth_ID column in the Bottle table has been synchronized with the Ship_Code column from the Cast Table.

14 May 2009

Correction were made to several 0707 bottle data records after comparison plots with CTD profiles identified flyer

1 Jan 2008

CalCOFI Data Reports and IEH ascii files include data above line 76.7 when collected (usually during the winter and spring CalCOFIs)

8 Sep 2006

Cruz_Sta value does not include Ship Code. Current format is CCYYMMLLLLSSSS where CC is century (19 or 20); YYMM is the usual year-month cruise designation (ex 0602); LLLL is Line; SSSS is Sta. Line & Sta format include the "tenths" value ie Lines are not rounded: line 93 is reported as 93.3, line 87 is 86.7. Santa Barbara Basin is 81.8 46.9, not 82 47. These changes were necessary to distinguish SCCOOS stations from standard stations. This change is reflected in the 0602 IEH file. Please note that pre-2008 IEH data does not include data collected above line 76.7. This allows data collected on different ships occupying the same station to link. Some older cruises performed the hydrographic work and biological work on separate ships.
Order_Occ column added to Cast table. This will be backfilled from the zooplankton database since IEH data does not include this value until 2000.

20 Jan 2006

Added a standard station field to the Station_ID table. ST in the Stnd_Sta column flags the current 66 quarterly-sampled stations.
Fixed Cast_Data Table: Cruz_Num & Int_Chl errors fixed. Parsing error combined the fields for several 80s cruises
Metafile Description - definitions and format
Design Notes - comments on establishing a standard format and tables for the 50+ years of data

Comments - CalCOFI 1949 - 2009 IEH-formatted ascii files are sorted by cruise, parsed into two comma-delimited ascii files (cast information; bottle data), combined with CalCOFI Data Report calculated values, then imported into Access 2003. Some common corrections are required: the cruise YYMM designation such as 9801 are extracted from the IEH header. If that field is empty (common in early IEHs) the cruise designation (variable Cruz_Nam) is generated from Year and Month automatically. Any query that uses the cruise designation (Cruz_Nam) may not pull all data collected from early cruises so use date and ship instead. Another note - Gulf of California station latitudes & longitudes generate negative Line.Sta numbers using the CalCOFI Line.Sta from Lat.Lon algorithm. These data are not excluded so the Line & Sta fields are not always numeric but text since a “G” designation is reported in many IEHs for those stations. See design notes for additional info.
JRW 2009

CSV's

For users who need comma-separated value files of CalCOFI hydrographic bottle data and station information (both are used to create the Access database). The CSV's include 1949-201004 published data (version 30Aug2010). Header information can be found on the database definitions webpage.

Hydrographic Bottle data can be found in the Bottle.csv.
Station information and primary productivity data can be found in the cast.csv.

Ascii IEH's

For users who need IEH's which contain CalCOFI hydrographic bottle and station information in ascii format. These are in CalCOFI 128-column data archive format and are available in 2 versions:

observed data (YYMMarch.ieh)
observed data with interpolated standard levels (YYMMt.ieh)

The IEH format was developed as an archive format for the CalCOFI data. Prior to Aug 1995, columns 64-65 contained format alignment characters (Z*). Starting in 2006, the Station Id will report Line & Sta to tenths ie 81.8 46.9 instead of 82 47 or 86.7 100.0 instead of 87 100. This change was made to allow the inclusion of coastal SCCOOS station data with nearby standard station data. (IEH stands for "Is Everybody Happy?" coined by programmer David Newton.)

Combined Cruise Hydrographic Data Reports

For older reports, visit our old site.

0901 Data Report : A compilation of the physical, chemical, and biological data for the Winter 2009 CalCOFI Cruise.

0810 Data Report : A compilation of the physical, chemical, and biological data for the Fall 2008 CalCOFI Cruise.

0808 Data Report : A compilation of the physical, chemical, and biological data for the Summer 2008 CalCOFI Cruise.

0804 Data Report : A compilation of the physical, chemical, and biological data for the Spring 2008 CalCOFI Cruise.

0801 Data Report : A compilation of the physical, chemical, and biological data for the Winter 2008 CalCOFI Cruise.

0711 Data Report : A compilation of the physical, chemical, and biological data for the Fall 2007 CalCOFI Cruise.

0707 Data Report : A compilation of the physical, chemical, and biological data for the Summer 2007 CalCOFI Cruise.

0704 Data Report: A compilation of the physical, chemical, and biological data for the Spring 2007 CalCOFI Cruise.

0701 Data Report: A compilation of the physical, chemical, and biological data for the Winter 2007 CalCOFI Cruise.

0610 Data Report: A compilation of the physical, chemical, and biological data for the Fall 2006 CalCOFI Cruise.

0607 Data Report: A compilation of the physical, chemical, and biological data for the Summer 2006 CalCOFI Cruise.

0604 Data Report: A compilation of the physical, chemical, and biological data for the Spring 2006 CalCOFI Cruise.

0602 Data Report: A compilation of the physical, chemical, and biological data for the Winter 2006 CalCOFI Cruise.

0511 Data Report: A compilation of the physical, chemical, and biological data for the Fall 2005 CalCOFI Cruise.

0507 Data Report: A compilation of the physical, chemical, and biological data for the Summer 2005 CalCOFI Cruise.

0504 Data Report: A compilation of the physical, chemical, and biological data for the Spring 2005 CalCOFI Cruise.

0501 Data Report: A compilation of the physical, chemical, and biological data for the Winter 2005 CalCOFI Cruise.

0411 Data Report: A compilation of the physical, chemical, and biological data for the Fall 2004 CalCOFI Cruise.

0407 Data Report: A compilation of the physical, chemical, and biological data for the Summer 2004 CalCOFI Cruise.

0404 Data Report: A compilation of the physical, chemical, and biological data for the Spring 2004 CalCOFI Cruise.

0401 Data Report: A compilation of the physical, chemical, and biological data for the Winter 2004 CalCOFI Cruise.

0310 Data Report: A compilation of the physical, chemical, and biological data for the Fall 2003 CalCOFI Cruise.

0307 Data Report: A compilation of the physical, chemical, and biological data for the Summer 2003 CalCOFI Cruise.

0304 Data Report: A compilation of the physical, chemical, and biological data for the Spring 2003 CalCOFI Cruise.

0302 Data Report: A compilation of the physical, chemical, and biological data for the Winter 2003 CalCOFI Cruise.

0207 and 0211 Data Report: A Compilation of the physical, chemical, and biological data for the Summer and Fall 2002 CalCOFI Cruise.

0201 and 0204 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 2002 CalCOFI Cruise.

0107 and 0110 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 2001 CalCOFI Cruise.

0101 and 0104 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 2001 CalCOFI Cruise.

0007 and 0010 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 2000 CalCOFI Cruise.

0001 and 0004 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 2000 CalCOFI Cruise.

9908 and 9910 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 1999 CalCOFI Cruise.

9901 and 9904 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 1999 CalCOFI Cruise.

9807 and 9809 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 1998 CalCOFI Cruise.

9802 and 9804 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 1998 CalCOFI Cruise.

9707 and 9709 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 1997 CalCOFI Cruise.

9702 and 9704 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 1997 CalCOFI Cruise.

9608 and 9610 Data Report: A compilation of the physical, chemical, and biological data for the Summer and Fall 1996 CalCOFI Cruise.

9602 and 9604 Data Report: A compilation of the physical, chemical, and biological data for the Winter and Spring 1996 CalCOFI Cruise.