Metadata Report for BODC Series Reference Number 1222972

Metadata Summary

Data Description

Data Category Surface temp/sal
Instrument Type
Turner 10-AU chlorophyll field fluorometer  fluorometers
Sea-Bird SBE 21 Thermosalinograph  thermosalinographs; water temperature sensor; salinity sensor
Trimble 4000DS Global Positioning System receiver  Differential Global Positioning System receivers
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Dr Tony Bale
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Project(s) Atlantic Meridional Transect (AMT)

Data Identifiers

Originator's Identifier AMT7_SURF
BODC Series Reference 1222972

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 1998-09-14 12:15
End Time (yyyy-mm-dd hh:mm) 1998-10-25 19:55
Nominal Cycle Interval 60.0 seconds

Spatial Co-ordinates

Start Latitude 50.80700 N ( 50° 48.4' N )
End Latitude 51.69190 S ( 51° 41.5' S )
Start Longitude 1.10500 W ( 1° 6.3' W )
End Longitude 57.82210 W ( 57° 49.3' 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)
ALATGP01 1 Degrees Lat_GPS Latitude north (WGS84) by unspecified GPS system
ALONGP01 1 Degrees Lon_GPS Longitude east (WGS84) by unspecified GPS system
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
FVLTTDZC 1 Dimensionless Fl_output_corr Instrument output (arbitrary scale) by autoranging chlorophyll fluorometer and correction to a common scale
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 AMT7 (JR34) Underway Surface Hydrography Data Quality Report

As described in the section on salinity calibration, there appeared to be a problem with the conductivity sensor during the cruise. The periods where this problem could be identified in the salinity channel were flagged as suspect. There may be other suspect sections that have not been identified. The salinity data should, therefore, be used with caution.

Due to the changing nature of the relationship between fluorometer output and chlorophyll-a concentrations, the data were split into different sections for the purposes of the calibration exercise. It is believed that this is the best way to produce an accurate representation of chlorophyll-a concentration throughout the cruise, but users who need accurate concentrations should use the extracted chlorophyll-a dataset directly.


Fofonoff, N.P. and Millard Jr., R.C., 1982. Algorithms for Computation of Fundamental Properties of Seawater. UNESCO Technical Papers in Marine Science, 44.

Data Access Policy

Public domain data

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

The recommended acknowledgment is

"This study uses data from the data source/organisation/programme, provided by the British Oceanographic Data Centre and funded by the funding body."

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 AMT7 (JR34) Underway Surface Hydrography Instrumentation Document

The instrumentation has been collated from various sources as historic notation of instrumentation was not well maintained. Care may be required if making assumptions based on the instruments used.

The following instruments were used for hydrographic measurements:

Instrument Name Model Serial Number Parameter(s)
Trimble 4000DS Global Positioning System receiver 4000DS N/A Latitude and Longtiude
Turner 10-AU chlorophyll field fluorometer Model 10 N/A Chlorophyll/Fluoresence
Sea-Bird SBE 21 Thermosalinograph SBE 21 N/A Temperature, Conductivity/Salinity, Pressure/Depth

RRS James Clark Ross Cruise AMT7 (JR34) Underway Surface Hydrography Data Processing Document

Originator's Data Processing

Raw data were logged as ADC counts on the ship's computers. They were converted into engineering units using initial manufacturers' calibrations. Conductivity and two temperature channels were produced from the thermosalinograph counts using laboratory calibrations on board ship.

The data from the fluorometer was logged into the JCR Ocean Logger system using the internal A/D converter and range output.

The data were submitted to BODC in RVS internal format for post-cruise processing and data banking.

BODC Data Processing


Underway data files were merged into a single binary merge file using time as the primary linking key. The time span of the file was from 13/09/1998 16:00:00 to 25/10/1998 19:55:00, with a sampling interval of 1 minute.

Salinity was computed from housing temperature and conductivity using the UNESCO 1978 Practical Salinity Scale (Fofonoff and Millard, 1982).


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.

Sample Calibrations


The underway sea temperature channel was compared with averaged surface values extracted from CTD profiles up to 7 metres. The 28 samples gave a small offset of 0.0101 °C between CTD and surface underway data with a standard deviation of 0.0228. As the offset was smaller than the standard deviation, no correction has been applied to the underway data.


It was not possible to calibrate the underway salinity channel as there are no available salinity sample data. The CTD salinity channel has itself not been calibrated. However, comparison of the two data sets can be made in order to test the consistency between the two channels. There were a number of occasions where the underway salinity was significantly different from the CTD salinity. Dates and times of these occasions are shown in the table below.

Date/time (GMT) Mean tsg salinity (PSU) No. values of values Mean CTD salinity to 7m (PSU) No. values of values Offset CTD - tsg (PSU)
22/09/1998 09:44 36.15 8 0.003 36.314 43 0 0.164
23/09/1998 09:17 36.578 8 0.005 36.675 41 0 0.097
25/09/1998 16:01 36.124 6 0.004 36.963 39 0.002 0.839
29/09/1998 10:14 36.13 6 0.005 36.365 26 0 0.235
16/10/1998 13:10 34.829 7 0.003 35.051 23 0 0.222

The salinity data were screened again, and it appeared that there may have been a problem with the conductivity sensor for some parts of the cruise. The following sections of the salinity record were flagged as suspect:

     18/09/1998 10:45 - 26/09/1998 03:10

     29/09/1998 08:14 - 30/09/1998 08:12

If the high offset values are excluded from the dataset, the remaining values (N=22) show a mean offset of 0.0044 PSU with a standard deviation of 0.011 PSU.


The data from the Turner Designs fluorometer suggested that the instrument was operated on the same range setting throughout the cruise.

The fluorometer voltage channel was compared with data obtained from fluorometric assays on acetone extracts from discrete underway samples throughout the cruise. This exercise showed a very inconsistent relationship between the two data sets. It is likely that the response of the instrument was affected by the very different oceanographic regimes encountered throughout the whole cruise. The data were examined carefully and split into different sections where the best relationships could be identified. Calibrations were then applied to different sections of the cruise. The relationship was of the form:

     Chlorophyll concentration (mg m-3) = fluorometer signal * coeffA + coeffB.

The effect of varying PAR was considered but no quenching effect could be identified.

Section start Section end coeffA coeffB R 2 No.samples
13/09/1998 16:00 16/09/1998 13:00 0.228 -0.196 69.2 13
16/09/1998 13:01 25/09/1998 15:47 0.350 -0.376 91.7 42
25/09/1998 15:48 29/09/1998 03:00 0.336 -0.337 90.4 34
29/09/1998 03:01 05/10/1998 15:00 0.493 -0.523 92.3 66
05/10/1998 15:01 10/10/1998 20:23 0.212 -0.265 70.7 57
10/10/1998 20:24 13/10/1998 17:40 0.227 -0.226 62.8 34
13/10/1998 17:41 15/10/1998 19:00 0.168 -0.191 89.8 23
15/10/1998 19:01 16/10/1998 23:29 0.145 -0.285 87.5 10
16/10/1998 23:30 25/10/1998 19:55 0.247 -0.166 55.6 39

Note that the data from the start of the cruise until 15/09/1998 01:00 showed a poor relationship with chlorophyll-a. The calibration equation obtained from the section 15/09/1998 14:00 to 16/09/1998 12:00 has been applied to the first section but users should not regard the first section as reliable data.


Fofonoff, N.P. and Millard Jr., R.C., 1982. Algorithms for Computation of Fundamental Properties of Seawater. UNESCO Technical Papers in Marine Science, 44.

SeaBird 21 SeaCAT Thermosalinograph SBE 21

The SBE21 is an externally powered instrument used to determine sea surface temperature and conductivity from underway vessels. Data is simultaneously stored in memory and output to a computer in real-time. Typically mounted on the ship's seawater intake, the SBE21 connects to an AC-powered interface box near a computer. TH interface box provides power and an isolated data interface, and contains a NMEA 0183 port for appending navigation data. There are options for auxiliary sensors using the RS-232 interface for a SBE32 temperature sensor and for four single-ended or two differential 0-5 volt A/D input channels for voltage output auxiliary sensors.

Components include internal-field conductivity cell eliminates proximity effects, which also permits use of expendable anti-foulant devices, for long-term bio-fouling protection. The thermistor is aged and pressure-protected.


  Conductivity Temperature, primary Temperature, SBE38 remote
Range 0 to 7 S/m -5 to 35°C -5 to 35°C
Initial Accuracy ±0.001 S/m ±0.01°C ±0.001°C
Resolution 0.000 S/m 0.001°C 0.0003°C

More information may be found in the SBE21 brochure .

Project Information

The Atlantic Meridional Transect (AMT) - Phase 1 (1995-2000)

Who was involved in the project?

The Atlantic Meridional Transect (AMT) programme was designed by and implemented as a collaboration between Plymouth Marine Laboratory (PML) and Southampton Oceanography Centre (SOC). The programme was hosted by Plymouth Marine Laboratory and involved additional researchers from UK and international universities throughout its duration.

What was the project about?

When AMT began in 1995 the programme provided a platform for international scientific collaboration, including the calibration and validation of SeaWiFs measurements and products. The programme provided an exceptional opportunity for nationally and internationally driven collaborative research and provided a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, the data collected by the AMT consortium informed on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.

The scientific aims were to assess:

When was the project active?

The first phase of the AMT programme ran from 1995 to 2000 and consisted of a total of 12 cruises. A second phase of funding allowed the project to continue for the period 2002 to 2006 with a further 6 cruises.

Brief summary of the project fieldwork/data

The AMT programme undertook biological, chemical and physical oceanographic research during the annual return passage of the RRS James Clark Ross between the UK and the Falkland Islands or the RRS Discovery between the UK and Cape Town, a distance of up to 13,500 km. This transect crossed a range of ecosystems from sub-polar to tropical and from euphotic shelf seas and upwelling systems to oligotrophic mid-ocean gyres. The transect route was covered north-south in September/October and south-north in April/May of each year.

The measurements of hydrographic and bio-optical properties, plankton community structure and primary production completed on the first 12 transects (1995-2000) represent the most coherent set of repeated biogeochemical observations over ocean basin scales. This unique dataset has led to several important discoveries concerning the identification of oceanic provinces, validation of ocean colour algorithms, distributions of picoplankton, identifying new regional sinks of pCO2 and variability in rates of primary production and respiration.

Who funded the project?

The programme was funded by the Natural Environment Research Council (NERC) and further support was received from the National Aeronautics and Space Administration (NASA) with equipment and funding from the Sea-viewing Wild Field-of-view Sensor (SeaWiFS) project.

Data Activity or Cruise Information


Cruise Name JR19980914 (AMT7, JR34)
Departure Date 1998-09-14
Arrival Date 1998-10-25
Principal Scientist(s)James Aiken (Plymouth Marine Laboratory)
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