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DataZoo

Tuesday, 02 December 2008 17:00 administrator

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)

Last Updated on Tuesday, 02 December 2008 22:48 Read more...

Available Data

Wednesday, 07 July 2004 01:54 administrator

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 07Dec09: 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 07 Dec 2009) bottle and station information csvs (final data only) exported from the research version of the Access database.
- Sql - (calcofi_iehdata_194903-200907SQL.zip) a sql dump of the web version of the database (final published data; from phpadmin/mysql).
CTD data - 1994 - 2009 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
Downloadable IEH ascii files (1949-2009). two versions: (YY=year, MM=month)

Last Updated on Monday, 07 December 2009 17:08 Read more...

CalCOFI Hydrographic Database

Tuesday, 10 February 2009 17:17 administrator

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 07Dec2009) 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. 07Dec2009)
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

Last Updated on Monday, 07 December 2009 17:12 Read more...

Bottle Data

Tuesday, 02 December 2008 16:39 administrator

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 07Dec09: 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 07 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

Last Updated on Monday, 07 December 2009 17:09 Read more...

CTD Data

Tuesday, 02 December 2008 16:38 administrator

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: 0907MH (Jul 2009 CalCOFI); latest bottle-corrected, combined data: 0907MH.

CTD Query Form - 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)

Last Updated on Monday, 07 December 2009 17:30 Read more...

Zooplankton

Tuesday, 02 December 2008 16:40 administrator

Zooplankton data are available through the Scripps Institution of Oceanography Pelagic Invertebrates Collection web page (Link) or DataZoo.

Last Updated on Thursday, 30 April 2009 15:49

Bird & Marine Mammal Data

Wednesday, 29 April 2009 17:12 administrator

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).

Bird and Marine Mammal Observation Census Data at DataZoo

Last Updated on Thursday, 30 April 2009 15:46

Hydrographic Database Query Form

Tuesday, 17 November 2009 17:18 administrator

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.

Last Updated on Tuesday, 17 November 2009 17:50

0804JD CTD Data

Monday, 24 August 2009 09:54 administrator

CalCOFI 0804JD CTD Data include 1m binavg bottle-corrected sensor data from leg 1 (25 Mar - 8 Apr) and leg 2 (23 - 30 Apr). SIO, NMFS & CDF&G scientists occupied 59 stations (Casts 1 - 59) on leg 1. On leg 2, there were twenty-one CTD stations (casts 60-80, order-occupied 150-177) including line 76.7 stations missed on leg 1. CTD, 12-10L rosette bottles, standard water sampling & analytical gear including electronic sample logger were provided by SIO-CalCOFI on both legs to insure continuity of line 76.7 and central coast data. Please refer to the Station Cast Description log for specific station date, time, and GPS coordinates. Click on the Line or Sta number listed below to download the station's CTD zip file (raw, asc, hdr, csv, & plot files) or click here for the complete cruise zip (0804CTDdata.zip).

**CalCOFI 0804JD CTD Stations & Sensor Data**
Cast	Line	Sta	Temp	Cond/Sal	O2	Trans	Fluor	ISUS	PAR	SPAR	Alt
Leg 1: 25 Mar - 8 Apr 2008
1	93.3	26.7	XX	XX	X	X	X	X?			X
2	93.4	26.4	XX	XX	X	X	X	X			X
3	91.7	26.4	XX	XX	X	X	X	X			X
4	93.3	28	XX	XX	X	X	X	X
5	93.3	30	XX	XX	X	X	X	X	X
6	93.3	35	XX	XX	X	X	X	X	X
7	93.3	40	XX	XX	X	X	X	X	X
8	93.3	45	XX	XX	X	X	X	X
9	93.3	50	XX	XX	X	X	X	X
10	93.3	55	XX	XX	X	X	X	X	X
11	93.3	60	XX	XX	X	X	X	X	X
12	93.3	70	XX	XX	X	X	X	X	X
13	93.3	80	XX	XX	X	X	X	X
14	93.3	90	XX	XX	X	X	X	X	X
15	93.3	100	XX	XX	X	X	X	X	X
16	93.3	110	XX	XX	X	X	X	X
17	93.3	120	XX	XX	X	X	X	X	X
18	90	120	XX	XX	X	X	X	X	X
19	90	110	XX	XX	X	X	X	X
20	90	100	XX	XX	X	X	X	X	X
21	90	90	XX	XX	X	X	X	X	X
22	90	80	XX	XX	X	X	X	X
23	90	70	XX	XX	X	X	X	X
24	90	60	XX	XX	X	X	X	X	X
25	90	53	XX	XX	X	X	X		X
26	90	45	XX	XX	X	X	X	X
27	90	37	XX	XX	X	X	X	X
28	90	35	XX	XX	X	X	X	X	X		X
29	90	30	XX	XX	X	X	X	X	X
30	90	28	XX	XX	X	X	X	X	X		X
31	86.7	33	XX	XX	X	X	X	X			X
32	86.7	35	XX	XX	X	X	X	X
33	86.7	40	XX	XX	X	X	X	X	X
34	86.7	45	XX	XX	X	X	X	X	X
35	86.7	50	XX	XX	X	X	X	X	X		X
36	86.7	55	XX	XX	X	X	X	X
37	86.7	60	XX	XX	X	X	X	X
38	86.7	70	XX	XX	X	X	X	X
39	86.7	80	XX	XX	X	X	X	X	X
40	86.7	90	XX	XX	X	X	X	X	X
41	86.7	100	XX	XX	X	X	X	X
42	86.7	110	XX	XX	X	X	X	X	X
43	83.3	110	XX	XX	X	X	X	X	X
44	83.3	100	XX	XX	X	X	X
45	83.3	90	XX	XX	X	X	X	X
46	83.3	80	XX	XX	X	X	X	X	X
47	83.3	70	XX	XX	X	X	X	X	X
48	83.3	60	XX	XX	X	X	X	X
49	83.3	55	XX	XX	X	X	X	X	X
50	83.3	51	XX	XX	X	X	X	X	X		X
51	83.3	42	XX	XX	X	X	X	X	X		X
52	83.3	40.6	XX	XX	X	X	X	X			X
53	81.8	46.9	XX	XX	X	X	X	X			X
54	80	51	XX	XX	X	X	X	X	X		X
55	76.7	49	XX	XX	X	X	X	X	X		X
56	80	55	XX	XX	X	X	X	X
57	80	60	XX	XX	X	X	X		X
58	80	70	XX	XX	X	X	X		X
59	80	80	XX	XX	X	X	X	X
Leg 2: 23 - 30 Apr 2008
150	76.7	51	XX	XX	X	X	X		X		X
151	76.7	55	XX	XX	X	X	X		X		X
152	76.7	60	XX	XX	X	X	X
153	76.7	70	XX	XX	X	X	X		X
154	76.7	80	XX	XX	X	X	X		X
160	76.7	90	XX	XX	X	X	X
161	76.7	100	XX	XX	X	X	X		X
162	73.3	90	XX	XX	X	X	X		X
164	73.3	80	XX	XX	X	X	X		X
165	73.3	70	XX	XX	X	X	X		X
166	73.3	60	XX	XX	X	X	X
167	73.3	55	XX	XX	X	X	X
168	70	55	XX	XX	X	X	X		X
169	70	60	XX	XX	X	X	X		X
170	66.7	50	XX	XX	X	X	X		X
172	66.7	55	XX	XX	X	X	X
173	66.7	60	XX	XX	X	X	X
174	66.7	65	XX	XX	X	X	X		X
175	66.7	70	XX	XX	X	X	X		X
176	66.7	75	XX	XX	X	X	X		X
177	66.7	80	XX	XX	X	X	X
	*1	*1	*2	*2				*3	*4	*5	*6

*1: Click on either line or sta number to download the station zip
*2: Two pairs of temperature & conductivity sensors plumbed on separate pumps
*3: ISUS NO3 sensor installed on leg 1 only (casts 1-59); no data on casts 25, 57, & 58
*4: PAR operational on all casts, no data on night stations
*5: Surface PAR data not available, not installed
*6: Altimeter operational on all casts but only detects bottom within ~50m

Last Updated on Friday, 28 August 2009 10:13

Scintillation Counter 2008

Tuesday, 30 June 2009 14:34 CalCOFI Technical Group

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.

Last Updated on Tuesday, 30 June 2009 15:04

CTD Asc Formats

Thursday, 02 July 2009 10:32 administrator

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.

Last Updated on Thursday, 02 July 2009 11:03

Change Timeline

Tuesday, 30 June 2009 14:29 administrator

Timeline of changes to data or methods

CTD Asc Filename Change

Tuesday, 30 June 2009 13:00 JRW

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.

Last Updated on Tuesday, 30 June 2009 15:03

CTD Asc Format Change

Tuesday, 30 June 2009 12:43 JRW

Voltage column headers in .asc files will be converted from "V0 V1 V2..." to sensor-specific labels. If V0 is transmissometer then the column header will be changed from "V0" to "TransV". Since the sensors can be mounted on different voltage channels on different cruises (or even the same cruise), this labeling scheme is important for easily distinguishing the sensor voltages. JRW 06/30/2009

Last Updated on Tuesday, 30 June 2009 15:03

CTD Notes

Tuesday, 30 June 2009 12:39 administrator

CTD Data and Format Notes

California Cooperative Oceanic Fisheries Investigations