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Metadata Report for BODC Series Reference Number 1359955

Metadata Summary

Data Description

Data Category Surface temp/sal
Instrument Type
SeaTech transmissometer  transmissometers
WET Labs {Sea-Bird WETLabs} WETStar fluorometer  fluorometers
Falmouth Scientific Instruments ocean temperature module  water temperature sensor
Falmouth Scientific Instruments ocean conductivity module  salinity sensor
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
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Atlantic Meridional Transect Phase2(AMT)

Data Identifiers

Originator's Identifier AMT17_PRODQXF_SURF
BODC Series Reference 1359955

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2005-10-15 08:25
End Time (yyyy-mm-dd hh:mm) 2005-11-26 05:50
Nominal Cycle Interval 60.0 seconds

Spatial Co-ordinates

Start Latitude 55.86700 N ( 55° 52.0' N )
End Latitude 35.46510 S ( 35° 27.9' S )
Start Longitude 4.35280 W ( 4° 21.2' W )
End Longitude 18.87120 E ( 18° 52.3' E )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 5.0 m
Maximum Sensor or Sampling Depth 5.0 m
Minimum Sensor or Sampling Height -
Maximum Sensor or Sampling Height -
Sea Floor Depth -
Sea Floor Depth Source -
Sensor or Sampling Distribution Fixed common depth - All sensors are grouped effectively at the same depth which is effectively fixed for the duration of the series
Sensor or Sampling Depth Datum Approximate - Depth is only approximate
Sea Floor Depth Datum -


BODC CODERankUnitsTitle
AADYAA011DaysDate (time from 00:00 01/01/1760 to 00:00 UT on day)
AAFDZZ011DaysTime (time between 00:00 UT and timestamp)
ALATGP011DegreesLatitude north relative to WGS84 by unspecified GPS system
ALONGP011DegreesLongitude east relative to WGS84 by unspecified GPS system
CPHLUMTF1Milligrams per cubic metreConcentration 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
CPHLUT011Milligrams per cubic metreConcentration 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
FVLTWS011VoltsRaw signal (voltage) of instrument output by linear-response chlorophyll fluorometer
PSALSG011DimensionlessPractical salinity of the water body by thermosalinograph and computation using UNESCO 1983 algorithm and calibration against independent measurements
TEMPHG011Degrees CelsiusTemperature of the water body by thermosalinograph hull sensor and verification against independent measurements
TVLTDR011VoltsRaw signal (voltage) of instrument output by 25cm path length red light transmissometer

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 Discovery AMT17 (D299) - Continuous Underway Hydrographic Data Quality Report

Two unusually large gaps in all meteorological and surface hydrography data streams occurred at the beginning of the cruise on 15/10/2005 between 08:40 and 16:00 and on 16/10/2005 between 11:48 and 15:41 GMT. These gaps are not mentioned in the cruise report. UKORS technical cruise report does mention that a new logging PC and device manager were being tried and this may explain the unusual problems.

N.B.The underway data finishes two days before the end of the cruise.


The fluorometer output fluctuated at the start and end of the cruise and it is during these periods there is the greatest scatter in the calibration residuals. There were many lower level (< 0.2 µg l-1) readings but fewer high level (> 0.4 µg l-1) extracted chlorophyll samples which may limit the accuracy of the calibrations at higher concentrations at the start and end of the cruise.

The fluorescence channel before calibration contains many negative values which have been flagged to advise the use of caution with these data. This is improved in the calibrated fluorescence channel.


The output voltage from the transmissometer still needs to have a calibration applied to generate the underway attenuance. No calibration equation was provided for the transmissometer. Open and blank voltage sheet for the cruise duration has been provided to BODC. Clear spikes in the transmissometer voltage channel have been flagged as improbable.

Temperature and Salinity

Instances where the underway supply was turned off have been flagged in both channels. These instances are evident by values which rise in a curve and then drop off. Flags applied by the data originator are present and have been applied to obvious spikes in the data.

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

WET Labs WETStar Fluorometers

WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.


By model:

  Chlorophyll WETStar CDOM WETStar Uranine WETStar Rhodamine WETStar Phycoerythrin WETStar
Excitation wavelength 460 nm 370 nm 485 nm 470 nm 525 nm
Emission wavelength 695 nm 460 nm 530 nm 590 nm 575 nm
Sensitivity 0.03 µg l-1 0.100 ppb QSD 1 µg l-1 - -
Range 0.03-75 µg l-1 0-100 ppb; 0-250 ppb 0-4000 µg l-1 - -

All models:

Temperature range 0-30°C
Depth rating 600 m
Response time 0.17 s analogue; 0.125 s digital
Output 0-5 VDC analogue; 0-4095 counts digital

Further details can be found in the manufacturer's specification sheet, and in the instrument manual.

SeaTech Transmissometer


The transmissometer is designed to accurately measure the the amount of light transmitted by a modulated Light Emitting Diode (LED) through a fixed-length in-situ water column to a synchronous detector.


  • Water path length: 5 cm (for use in turbid waters) to 1 m (for use in clear ocean waters).
  • Beam diameter: 15 mm
  • Transmitted beam collimation: <3 milliradians
  • Receiver acceptance angle (in water): <18 milliradians
  • Light source wavelength: usually (but not exclusively) 660 nm (red light)


The instrument can be interfaced to Aanderaa RCM7 current meters. This is achieved by fitting the transmissometer in a slot cut into a customized RCM4-type vane.

A red LED (660 nm) is used for general applications looking at water column sediment load. However, green or blue LEDs can be fitted for specilised optics applications. The light source used is identified by the BODC parameter code.

Further details can be found in the manufacturer's Manual.

Falmouth Scientific Inc. Ocean Sensor Modules

FSI's individual sensor modules include an Ocean Conductivity Module (OCM), Ocean Temperature Module (OTM) and Ocean Pressure Module (OPM). All three use a low power micro-controller to collect, scale and transmit real-time data via RS-232 or RS-485.

Parameter OCM Conductivity OTM Temperature OPM Pressure
Range 0 - 7.0 S/m(0 - 70 mS/cm) -2 to 32 °C User Specified:0-200 dBar0-1000 dBar0-2000 dBar0-3000 dBar0-7000 dBar
Accuracy -0.0003* S/m(-0.003 mS/cm) -0.003 °C* -0.03% full scale*
Stability /month -0.00005 S/m(-0.0005 mS/cm) -0.0005 °C -0.002% full scale
Resolution 0.00001 S/m(-0.0001 mS/cm) 0.0001 °C 0.0004% full scale
Response at 1 m/s flow 50 msec 150 msec 25 msec
Sensor Type Inductive cell Platinum thermometer Strain gauge

* Higher accuracy available

For further details, see the manufacturer's specification sheet.

RRS Discovery AMT17 (D299) - Continuous Underway Hydrographic Instrumentation Document

Manufacturer Model Main Function Serial Number Comments
Trimble 4000DS Position (Latitude and Longitude) - -
WETLABS W3S Fluorometer 246 -
FSI OTM Temperature 1360 Hull sensor temperature
FSI OCM Conductivity/Salinity 1376 Non-toxic supply
Seatech - Transmissometer 114R -

RRS Discovery AMT17 (D299) - Continuous Underway Hydrographic Processing Documentation

Originator's Processing

SurfMet, the UKORS surface water and meteorological suite of instrumentation was run for the duration of the cruise and logged the data to the RVS file 'surfmet'. The temperature and conductivity data were used to calculate the surface salinity and were logged in the RVS file 'protsg'. The transmissometer and fluorometer flow loop was stopped occasionally to clean the transmissometer lenses and take air and blank readings.

BODC Data Processing


Data from the full-resolution RVS files were converted to ASCII format and then transferred to BODC's NetCDF format (QXF) under the BODC Underway Data System (BUDS). This transfer involved reducing the data to 60 second intervals using averaging. Directional data were reduced by averaging using a unit circle.


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.

Data processing

The data were loaded from the files 'protsg' and 'surfmet'.

Relative wind speed and direction were logged from the meteorological package during the cruise. The anemometer was positioned with 0 degrees at the ship's stern. The ship's speed relative to the ground was calculated at BODC using the ship's navigational information and the ship's heading. The speed and heading were then used to correct the wind data for the effect of the ship's movement. Absolute wind speed and direction channels were created.

The raw voltage channels were transferred for the PAR and TIR sensors. These channels were converted to Wm-2 using the calibration coefficients from the calibration certificates supplied to BODC by UKORS. For the PAR sensors the conversion was 1 mV = 100 Wm-2 (conversion x105) and for the TIR sensors the conversion was 1 µV = 1 Wm-2(conversion x106).

The raw voltage channels for the fluorometer and transmissometer were transferred and converted from mV to V (conversion factor x0.001). Data were flagged for periods where the non-toxic supply was turned off and for spikes associated with cleaning operations.



Salinity data from the thermosalinograph were compared with bench salinometer readings for samples taken from the ship's non-toxic pumped sea water supply. A drift in the offset was noticed for the readings from 04/11/2005 18:09 until the end of the cruise and calibration equations for each of three separate periods were derived using a linear interpolation against time. The CTD sensor calibration data had not displayed the same drift and therefore it was felt the drift was in the thermosalinograph not the bench salinometer data. The cruise was split into 3 sections and linear calibrations made for the offset against decimalised time for each period. The first period related to the section until the ship arrived in Ponta Delgada for the second time. The second section ran from the ship leaving Ponta Delgada for the second time until a step in the underway sensor salinity of 0.2 PSU with no matching jump in temperature (SST or TSG). The final section of the cruise runs from this step in the salinity until the cruise ended.

The root mean square (RMS) error for the calibration dataset was calculated between the bench salinometer data and both the uncalibrated TSG and the calibrated salinity.

  Uncalibrated Salinity Calibrated Salinity
Max Offset -0.050 0.028
Min Offset -0.191 -0.016
RMS 0.149 0.008

The decrease in the RMS error indicates the calibration improves the match between the bench salinometer and the TSG sensor. Once the calibration was applied the average offset (bench salinometer-calibrated TSG) was -2.5x10-5, with SD = 0.008.

Start Date/Time End Date/Time Calibration Type Offset Value (Start) Offset Value (End) N R2 (%) BODC ICALRF
17/10/2005 12:00 25/10/2005 09:58 Linear offset with time -0.1754 -0.1513 8 82.67 6197
27/10/2005 10:45 04/11/2005 18:09 Linear offset with time -0.1516 -0.1976 13 65.98 6198
04/11/2005 18:09 26/11/2005 06:00 Linear offset with time -0.1961 -0.0404 31 96.06 6199


The parameter TEMPCU01 was taken from the CTD profiles and TEMPHU01 from the underway files. The data from the CTD profiles were averaged over 5 decibars. Data values with high standard deviations were removed from the calibration set and the offset was calculated from CTD temp - hull sensor temp. The offset was then plotted against time and CTD temperature. There was a significant regression with time but not with CTD temperature. A linear offset was calculated against cruise time and values determined for the offset at the start and end of the cruise. The BODC calibration system then generated the offset to be added for each time interval in between.

The root mean square (RMS) error was calculated for the comparison of surface temperature from the SeaBird CTD with the uncalibrated TSG temperature and the newly calibrated temperature for the calibration dataset.

  Uncalibrated Temperature Calibrated Temperature
Max Offset -0.003 0.026
Min Offset -0.088 -0.053
RMS -0.0314 0.0132

The decrease in the RMS error indicates the calibration improves the match between the CTD temperature and the hull temperature sensors. Once the calibration was applied the average offset (CTD-calibrated) was 2x10-5 °C, with SD = 0.01 °C.

Start Date/Time End Date/Time Calibration Type Offset Value (Start) Offset Value (End) N R2 (%) BODC ICALRF
16/10/2005 08:00 26/10/2005 08:00 Linear offset with time -0.0107 -0.0426 44 21.2 6203


The fluorometer channel (FVLTWS01) was calibrated by converting the voltage to a nominal chlorophyll concentration (CPHLUMTF) using the calibration equation provided by UKORS.

CPHLUMTF = 13.1 * FVLTWS01 - 1.0349 (BODC ICALRF = 6207)

The nominal chlorophyll concentration values were compared to discrete chlorophyll concentrations, which were extracted after samples from the ship's non-toxic water supply, filtered and then dissolved in acetone and analysed against known chlorophyll-a standards with a bench fluorometer. The cruise was broken up into 5 sections based on changes in the fluorometer readings before and after the ship had been alongside for repairs and the presence of 'steps' in the fluorometer readings. The first and last sections had offsets that were significantly related to the extracted chlorophyll data and in for these periods a calibration equation was applied. The three middle sections showed a significant linear regression between the offset and time. In these cases offset values were generated for the start and end of each period and the BODC calibration form applied the appropriate offset for the period in between. The calibrations and the periods for which they have been applied are given in the table below. These adjustments were made to generate the final calibrated channel (CPHLUT01).

Start Date/Time End Date/Time Calibration Type N R2 (%) BODC ICALRF
16/10/2005 08:00 25/10/2005 07:00 Linear offset with time 28 61.24 6406
17/11/2005 04:30 26/11/2005 06:00 Linear offset with time 46 68.27 6407
Start Date/Time End Date/Time Calibration Type Offset Value (Start) Offset Value (End) N R2 (%) BODC ICALRF
27/10/2005 09:00 01/11/2005 07:05 Linear offset with time 0.5868 0.6818 23 36.3 6208
01/11/2005 07:10 04/11/2005 15:55 Linear offset with time 0.4870 0.6228 13 85.3 6209
04/11/2005 15:55 16/11/2005 21:15 Linear offset with time 0.4723 0.7074 51 68.6 6210

The root mean square (RMS) error for the calibration dataset was calculated for offset between the discrete extracted samples and both the nominal fluorometer values and the newly calibrated fluorometer values.

  Nominal calibration Sample calibration
Max Offset 0.774 0.644
Min Offset -1.411 -0.138
RMS 0.596 0.064

The decrease in the RMS error indicates the calibration improves the match between the extracted chlorophyll values and the fluorometer values. Once the calibration was applied the average offset (Extracted chl-a - calibrated fluorometer) was 0.0004 mg m-3, with SD = 0.064 mg m-3.

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:

  • University of Liverpool
  • University of Newcastle
  • University of Plymouth
  • University of Southampton
  • University of East Anglia

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:

  • how the structure, functional properties and trophic status of the major planktonic ecosystems vary in space and time
  • how physical processes control the rates of nutrient supply to the planktonic ecosystem
  • how atmosphere-ocean exchange and photo-degradation influence the formation and fate of organic matter

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 D299 (AMT17)
Departure Date 2005-10-15
Arrival Date 2005-11-28
Principal Scientist(s)Patrick M Holligan (University of Southampton School of Ocean and Earth Science)
Ship RRS Discovery

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
B nominal value
Q value below limit of quantification