Metadata Report for BODC Series Reference Number 1359851

Metadata Summary

Data Description

Data Category Surface temp/sal
Instrument Type
Sea-Bird SBE 45 MicroTSG thermosalinograph  thermosalinographs; water temperature sensor; salinity sensor
Turner 10-AU chlorophyll field fluorometer  fluorometers
Trimble 4000DS Global Positioning System receiver  Differential Global Positioning System receivers
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Prof Patrick Holligan
Originating Organization University of Southampton School of Ocean and Earth Science
Processing Status banked
Project(s) Atlantic Meridional Transect Phase2(AMT)

Data Identifiers

Originator's Identifier AMT14_PRODQXF_SURF
BODC Series Reference 1359851

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2004-04-28 19:12
End Time (yyyy-mm-dd hh:mm) 2004-05-30 15:11
Nominal Cycle Interval 60.0 seconds

Spatial Co-ordinates

Southernmost Latitude 51.69165 S ( 51° 41.5' S )
Northernmost Latitude 49.38265 N ( 49° 23.0' N )
Westernmost Longitude 57.82399 W ( 57° 49.4' W )
Easternmost Longitude 5.76652 W ( 5° 46.0' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor Depth 6.0 m
Maximum Sensor Depth 6.0 m
Minimum Sensor Height -
Maximum Sensor Height -
Sea Floor Depth -
Sensor Distribution Fixed common depth - All sensors are grouped effectively at the same depth which is effectively fixed for the duration of the series
Sensor Depth Datum Approximate - Depth is only approximate
Sea Floor Depth Datum -


BODC CODE Rank Units Short Title Title
AADYAA01 1 Days Date(Loch_Day) Date (time from 00:00 01/01/1760 to 00:00 UT on day)
AAFDZZ01 1 Days Time(Day_Fract) Time (time between 00:00 UT and timestamp)
ALATTR01 1 Degrees Lat_TrimbleGPS Latitude north (WGS84) by Trimble GPS
ALONTR01 1 Degrees Lon_TrimbleGPS Longitude east (WGS84) by Trimble GPS
CPHLUMTF 1 Milligrams per cubic metre chl-a_water_NTTFfluor_manufctrcal Concentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by through-flow fluorometer plumbed into non-toxic supply and manufacturer's calibration applied
CPHLUT01 1 Milligrams per cubic metre chl-a_water_NTTFfluor_sampcal Concentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by through-flow fluorometer plumbed into non-toxic supply and calibration against sample data
PSALSG01 1 Dimensionless P_sal_TSG_calib Practical salinity of the water body by thermosalinograph and computation using UNESCO 1983 algorithm and calibration against independent measurements
TEMPSG01 1 Degrees Celsius CalTSGTmp Temperature of the water body by thermosalinograph and verification against independent measurements

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

Problem Reports

No Problem Report Found in the Database

RRS James Clark Ross Cruise AMT14 (JR20040428) - Underway Hydrography Data Quality Report

A few periods during the dataset and a few spikes considered suspect were flagged 'M'.

PSALSGU01 data below the Limit for detection of the parameter have been flagged as Null. These data occurred at the start of the dataset till 19:45:00 28/04/2004.

Data Access Policy

Open Data supplied by Natural Environment Research Council (NERC)

You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."

Narrative Documents

Turner Designs 10AU Field Fluorometer

The Turner Designs 10AU is designed for continuous-flow monitoring or discrete sample analyses of fluorescent species. A variety of optical kits with appropriate filters and lamps are available for a wide range of applications. Individual filters and lamps are also available for customised applications.

Standard optical kits include those for chlorophyll- a (extracted and/or in vivo ), phycocyanin, phycoerythrin, CDOM, ammonium, rhodamine and fluorescein dye tracing, crude oil, refined oil, histamine and optical brighteners.

The instrument's light source is a 4 watt lamp and the detector is a photomultiplier tube with a standard detection range of 300-650 nm. A red-sensitive version with a detetion range of 185-970 nm is also available.


Operating temperature 0 to 55°C
Detector PhotoMultiplier Tube

300 to 650 nm (standard)

185 to 870 nm (Red)

Detection Limits:
Extracted Chlorophyll- a
Rhodamine WT Dye
Fluorescein Dye

0.025 µg L -1
0.01 ppb (in potable water)
0.01 ppb (in potable water)
Linear range:
Extracted Chlorophyll- a
Rhodamine WT Dye
Fluorescein Dye

0 to 250µg L -1
0 to 250 ppb
0 to 250 ppb

Further details can be found in the manufacturer's specification sheet .

Trimble 4000DS Global Positioning System receiver

The Trimble 4000DS Differential Surveyor is similar to the 4000RS (a Maxwell-based receiver that is oriented toward precision positioning applications. It is intended for use as a DGPS base station, generating RTCM-104 corrections). The 4000Ds can apply RTCM-104 corrections to the satellite data it receives in order to generate accurate position fixes in real time.

RRS James Clark Ross Cruise AMT14 (JR20040428) - Underway Hydrography Instrumentation Document

The following instruments were used to obtain hydrographic measurements:

Manufacturer Model Main Function Serial Number Comments
Trimble 4000DS Position (Latitude and Longitude) - -
Turner Instruments 10AU Fluorometer 005-CE -
SeaBird SBE45 Salinity - Conductivity 0 - 7 S m -1
Temperature - -5 - 35°C

SeaBird MicroTSG Thermosalinograph SBE 45

The SBE45 MicroTSG is an externally powered instrument designed for shipboard measurement of temperature and conductivity of pumped near-surface water samples. The instrument can also compute salinity and sound velocity internally.

The MicroTSG comprises a platinum-electrode glass conductivity cell and a stable, pressure-protected thermistor temperature sensor. It also contains an RS-232 port for appending the output of a remote temperature sensor, allowing for direct measurement of sea surface temperature.

The instrument can operate in Polled, Autonomous and Serial Line Sync sampling modes:


  Conductivity Temperature Salinity
Range 0 to 7 Sm -1 -5 to 35°C  
Initial accuracy 0.0003 Sm -1 0.002°C 0.005 (typical)
Resolution 0.00001 Sm -1 0.0001°C 0.0002 (typical)
Typical stability (per month) 0.0003 Sm -1 0.0002°C 0.003 (typical)

Further details can be found in the manufacturer's specification sheet .

RRS James Clark Ross Cruise AMT14 (JR20040428) - Underway Hydrography Processing Document

Originator's Data Processing

The raw data were logged every second to the SCS logging system. The latitude and longitude navigation data originated from the Trimble 4000DS Trimble Surveyor system using Marine Star differential corrections.

The data were submitted to BODC in ASCII output from the BAS SCS system for post-cruise processing and data banking.

BODC Data Processing


Data from the full-resolution SCS files were transferred to BODC's NetCDF format QXF under the BODC Underway Data System (BUDS). The transfer involved reducing the data to 60 second intervals.


Each data channel was inspected on a graphics workstation and any spikes or periods of dubious data were flagged. The power of the workstation software was used to carry out comparative screening checks between channels by overlaying data channels. A map of the cruise track was simultaneously displayed in order to take account of the oceanographic context.

Values that were outside the parameters designated limits for detection were flagged 'M'.

Data processing, correction and calibration

Navigational data were available from three different systems on the JCR. These were screened in order to select the best quality data for the primary navigation channels. The data from the Trimble GPS system were consistently good and showed no spikes.

A program was run which located any null values in the latitude and longitude channels and checked to ensure that the ship's speed did not exceed 15 knots. There was 1 speed check failures in the Trimble navigation data and 2 small gaps. These points were screened again to look for improbable spikes which were flagged as null. The gaps were then filled using linear interpolation.


TSG temperature was checked against the CTD temperature measurements averaged over the upper 6 m of the water column. Only CTD data points with a standard deviation (SD)< 0.01 °C in the upper 6 m and underway records with SD< 0.01°C over the duration of the cast were considered. Based on a total of 23 paired samples, the diffference between the TSG and the CTD values averaged 0.00 degree C ±0.03 and ranged between -0.08 and 0.05°C with no obvious trend. No correction was applied to the TSG channel.


Salinity data from the thermosalinograph have been compared with calibrated surface CTD data to a depth of 20 m. This is usually done to a depth of 6 m, however, the CTD data down to 6 m depth are suspect. There was no time information for water samples so used calibrated CTD to calibrate the underway salinity. However, there were no data for CTD salinity down to 6 m depth - the value usually used in the function 'intcal' to average the CTD salinities. Different averaging depths (6 m, 10 m, 15 m and 20 m) were investigated and it was found that it was needed to average 20 m of CTD salinity data. Comparison of all depth averages to the underway data shows that there is no adverse effect in increasing the depth averaging window to 20 m. It was therefore decided to calibrate the underway salinity data to the calibrated CTD data averaged over 20 m depth. The underway data were averaged over the period of CTD deployments and standard deviations were used to check the quality of the data. The 84 samples showed the following relationship, which has been used to produce a calibrated temperature channel (PSALSG01).

PSALSG01 = 0.994056 * PSALSU01 + 0.225660 (BODC calibration reference 3796)


The fluorometer channel was calibrated by comparing the uncalibrated fluorometer output with chlorophyll concentration values extracted from samples collected from the ship's non-toxic water supply (N=263). The relationship between extracted and fluorometer values was reasonable (R 2 =0.76) and apparently unskewed.

The following equation was derived by linear regression:

CPHLUT01 = 1.861 (±0.065) * CPHLUMTF - 0.098 (±0.012), R2=0.76

Residuals (extracted chlorophyll from the non-toxic minus calibrated fluorometer) follow a normal distribution and range between -0.73 and 0.53 mg chl m -3 for chlorophyll concentrations ranging from 0.09 to 1.48 mg Chla m -3 . The largest variations are due to a peak in the chlorophyll concentration values around 16/05/2004 which is not present in the fluorometer readings.

Project Information

The Atlantic Meridional Transect - Phase 2 (2002-2006)

Who was involved in the project?

The Atlantic Meridional Transect Phase 2 was designed by and implemented by a number of UK research centres and universities. The programme was hosted by Plymouth Marine Laboratory in collaboration with the National Oceanography Centre, Southampton. The universities involved were:

What was the project about?

AMT began in 1995, with scientific aims to assess mesoscale to basin scale phytoplankton processes, the functional interpretation of bio-optical signatures and the seasonal, regional and latitudinal variations in mesozooplankton dynamics. In 2002, when the programme restarted, the scientific aims were broadened to address a suite of cross-disciplinary questions concerning ocean plankton ecology and biogeochemistry and the links to atmospheric processes.

The objectives included the determination of:

The data were collected with the aim of being distributed for use in the development of models to describe the interactions between the global climate system and ocean biogeochemistry.

When was the project active?

The second phase of funding allowed the project to continue for the period 2002 to 2006 and consisted of six research cruises. The first phase of the AMT programme ran from 1995 to 2000.

Brief summary of the project fieldwork/data

The fieldwork on the first three cruises was carried out along transects from the UK to the Falkland Islands in September and from the Falkland Islands to the UK in April. The last three cruises followed a cruise track between the UK and South Africa, only deviating from the traditional transect in the southern hemisphere. During this phase the research cruises sampled further into the centre of the North and South Atlantic Ocean and also along the north-west coast of Africa where upwelled nutrient rich water is known to provide a significant source of climatically important gases.

Who funded the project?

Natural Environment Research Council (NERC)

Data Activity or Cruise Information


Cruise Name JR20040428 (AMT14, JR101)
Departure Date 2004-04-28
Arrival Date 2004-06-01
Principal Scientist(s)Patrick M Holligan (University of Southampton School of Ocean and Earth Science)
Ship RRS James Clark Ross

Complete Cruise Metadata Report is available here

Fixed Station Information

No Fixed Station Information held for the Series

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Flag Description
Blank Unqualified
< Below detection limit
> In excess of quoted value
A Taxonomic flag for affinis (aff.)
B Beginning of CTD Down/Up Cast
C Taxonomic flag for confer (cf.)
D Thermometric depth
E End of CTD Down/Up Cast
G Non-taxonomic biological characteristic uncertainty
H Extrapolated value
I Taxonomic flag for single species (sp.)
K Improbable value - unknown quality control source
L Improbable value - originator's quality control
M Improbable value - BODC quality control
N Null value
O Improbable value - user quality control
P Trace/calm
Q Indeterminate
R Replacement value
S Estimated value
T Interpolated value
U Uncalibrated
W Control value
X Excessive difference

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Flag Description
0 no quality control
1 good value
2 probably good value
3 probably bad value
4 bad value
5 changed value
6 value below detection
7 value in excess
8 interpolated value
9 missing value
A value phenomenon uncertain