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Metadata Report for BODC Series Reference Number 867895

Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
Neil Brown MK3 CTD  CTD; water temperature sensor; salinity sensor; dissolved gas sensors
SeaTech transmissometer  transmissometers
Chelsea Technologies Group Aquatracka fluorometer  fluorometers
Chelsea Technologies Group 2-pi PAR irradiance sensor  radiometers
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Dr Ian Joint
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) OMEX II-II

Data Identifiers

Originator's Identifier CTDAB
BODC Series Reference 867895

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 1998-08-10 04:54
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 2.0 decibars

Spatial Co-ordinates

Latitude 41.90850 N ( 41° 54.5' N )
Longitude 9.32033 W ( 9° 19.2' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 6.95 m
Maximum Sensor or Sampling Depth 151.75 m
Minimum Sensor or Sampling Height 12.94 m
Maximum Sensor or Sampling Height 157.75 m
Sea Floor Depth 164.7 m
Sea Floor Depth Source -
Sensor or Sampling Distribution Variable common depth - All sensors are grouped effectively at the same depth, but this depth varies significantly during the series
Sensor or Sampling Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface


BODC CODERankUnitsTitle
ATTNZR011per metreAttenuation (red light wavelength) per unit length of the water body by transmissometer
CPHLPR011Milligrams per cubic metreConcentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer
FVLTAQ011VoltsRaw signal (voltage) of instrument output by in-situ Aquatracka chlorophyll fluorometer
LVLTPD011VoltsRaw signal (voltage) of instrument output by PML/Chelsea Instruments 2-pi PAR downwelling light meter
LVLTPU011VoltsRaw signal (voltage) of instrument output by PML/Chelsea Instruments 2-pi PAR upwelling light meter
NVLTST011VoltsRaw signal (voltage) of instrument output by SeaTech light backscatter nephelometer (LBSS)
POATCV011per metrePotential attenuance (unspecified wavelength) per unit length of the water body by transmissometer and computation using P-EXEC algorithm
POTMCV011Degrees CelsiusPotential temperature of the water body by computation using UNESCO 1983 algorithm
PRESPR011DecibarsPressure (spatial coordinate) exerted by the water body by profiling pressure sensor and correction to read zero at sea level
PSALST011DimensionlessPractical salinity of the water body by CTD and computation using UNESCO 1983 algorithm
SIGTPR011Kilograms per cubic metreSigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm
TEMPST011Degrees CelsiusTemperature of the water body by CTD or STD

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

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

Neil Brown MK3 CTD

The Neil Brown MK3 conductivity-temperature-depth (CTD) profiler consists of an integral unit containing pressure, temperature and conductivity sensors with an optional dissolved oxygen sensor in a pressure-hardened casing. The most widely used variant in the 1980s and 1990s was the MK3B. An upgrade to this, the MK3C, was developed to meet the requirements of the WOCE project.

The MK3C includes a low hysteresis, titanium strain gauge pressure transducer. The transducer temperature is measured separately, allowing correction for the effects of temperature on pressure measurements. The MK3C conductivity cell features a free flow, internal field design that eliminates ducted pumping and is not affected by external metallic objects such as guard cages and external sensors.

Additional optional sensors include pH and a pressure-temperature fluorometer. The instrument is no longer in production, but is supported (repair and calibration) by General Oceanics.


These specification apply to the MK3C version.

Pressure Temperature Conductivity

6500 m

3200 m (optional)

-3 to 32°C 1 to 6.5 S cm-1

0.0015% FS

0.03% FS < 1 msec


0.003°C < 30 msec

0.0001 S cm-1

0.0003 S cm-1 < 30 msec

Further details can be found in the specification sheet.

Aquatracka fluorometer

The Chelsea Instruments Aquatracka is a logarithmic response fluorometer. It uses a pulsed (5.5 Hz) xenon light source discharging between 320 and 800 nm through a blue filter with a peak transmission of 420 nm and a bandwidth at half maximum of 100 nm. A red filter with sharp cut off, 10% transmission at 664 nm and 678 nm, is used to pass chlorophyll-a fluorescence to the sample photodiode.

The instrument may be deployed either in a through-flow tank, on a CTD frame or moored with a data logging package.

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

Chelsea Technologies Photosynthetically Active Radiation (PAR) Irradiance Sensor

This sensor was originally designed to assist the study of marine photosynthesis. With the use of logarithmic amplication, the sensor covers a range of 6 orders of magnitude, which avoids setting up the sensor range for the expected signal level for different ambient conditions.

The sensor consists of a hollow PTFE 2-pi collector supported by a clear acetal dome diverting light to a filter and photodiode from which a cosine response is obtained. The sensor can be used in moorings, profiling or deployed in towed vehicles and can measure both upwelling and downwelling light.


Operation depth 1000 m
Range 2000 to 0.002 µE m-2 s-1
Angular Detection Range ± 130° from normal incidence
Relative Spectral Sensitivity

flat to ± 3% from 450 to 700 nm

down 8% of 400 nm and 36% at 350 nm

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

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.

RRS Charles Darwin 114 CTD Data Documentation

Instrumentation and Shipboard Procedures


The CTD profiles were taken with a Neil Brown Systems Mk IIIB CTD including a pressure sensor, a conductivity cell, a platinum resistance thermometer and a Beckmann dissolved oxygen sensor. The latter returned no useful data for this cruise.

The CTD unit was mounted vertically in the centre of a protective cage approximately 2m square.

The following instruments were also attached to the bars of the cage and logged as additional CTD channels:

  • Chelsea Instruments Aquatracka configured as a fluorometer.
  • SeaTech light backscatter sensor (LBSS nephelometer).
  • SeaTech 20-cm path-length red (661 nm) light transmissometer.
  • PML 2 PAR (photosynthetically available radiation) scalar irradiance sensors configured to measure downwelling and upwelling radiation.

Note that the downwelling light sensor was actually mounted on a pole placing it in line with the top of the water bottle rosette, 1.75 m above the pressure head. As a result, there was a vertical separation of some two metres between the upwelling and downwelling sensor positions. No geometrical correction of the light data has been attempted.

A General Oceanics 24-bottle tone-fire rosette pylon was fitted to the top of the CTD frame. 10-litre lever-action or externally sprung Niskin bottles were used throughout the cruise.

Data Acquisition

On each cast, the CTD was lowered continuously at 0.5 to 1.0 m s-1 to the closest comfortable proximity to the sea floor. The upcast was done in stages between the bottle firing depths. A tone fire system was installed to minimise the disruption caused to the data stream by the bottle-firing signal.

The data were logged by the RVS ABC data logging system. Output channels from the deck unit were logged at 32 Hz by a microprocessor interface (the Level A) which passed time-stamped averaged cycles at 1 Hz to a Sun workstation (the Level C) via a buffering system (the Level B).

On-Board Data Processing

The raw data comprised ADC counts. These were converted into engineering units (volts for PAR meters, fluorometer LBSS and transmissometers; ml l-1 for oxygen; mmho cm-1for conductivity; °C for temperature; decibars for pressure) by the application of laboratory determined calibrations. Salinity (Practical Salinity Units as defined in Fofonoff and Millard, 1982) was calculated using the standard UNESCO function from the conductivity ratio (conductivity/42.914) and a time lagged temperature.

The data set was submitted to BODC in this form on Quarter Inch Cartridge tapes in RVS internal format for post-cruise processing and data banking.

Post-Cruise Processing and Calibration at BODC


The data were converted into the BODC internal format to allow the use of in-house software tools, notably the workstation graphics editor. In addition to reformatting, the transfer program applied the following modifications to the data:

  • Dissolved oxygen was converted from ml/l to µM by multiplication by 44.66.
  • Transmissometer voltages were corrected to the manufacturer's specified voltage by ratio using transmissometer air readings taken during the cruise (see the calibration section for details). The voltages were then converted to percentage transmission by multiplying them by 20 and to attenuance using the algorithm:
attenuance (m-1) = -5 loge (% transmission/100)


Reformatted CTD data were transferred onto a high-speed graphics workstation. Using custom in-house graphics editors, downcasts and upcasts were differentiated and the limits of the downcasts and upcasts were manually flagged.

Spikes on all the downcast channels were manually flagged. No data values were edited or deleted; flagging was achieved by modification of the associated quality control flag.

The pressure ranges over which the bottle samples had been collected were logged by manual interaction with the software. Usually, clusters of points recorded while the CTD was held stationary were used to determine this. These pressure ranges were subsequently used, in conjunction with a geometrical correction for the position of the water bottles with respect to the CTD pressure transducer, to determine the pressure range of data to be averaged for calibration values.

Once screened on the workstation, the CTD downcasts were loaded into a database under the ORACLE Relational Database Management System. 49 casts were loaded from leg A, including a yo-yo cast that has been loaded to the system as a further 34 casts. 34 casts were loaded from leg B. These were later migrated to the National Oeanographic Database.


With the exception of pressure, calibrations were done by comparison of CTD data against measurements made on water bottle samples or from the reversing thermometers mounted on the water bottles as in the case of temperature. In general, values were averaged from the CTD downcasts but where visual inspection of the data showed significant hysteresis values were manually extracted from the CTD upcasts.

All calibrations described here have been applied to the data.


The pressure calibration was derived by averaging pressures logged in air. The data from leg A showed a clear bimodal distribution. Consequently, two calibrations were produced.

The mean corrections obtained were:

Leg A (CTD01-CTD08): Corrected pressure = Raw pressure + 3.77 (SD 0.27)
Leg A (CTD09-CTD49): Corrected pressure = Raw pressure + 2.81 (SD 0.34)
Leg B (CTD50-CTD83): Corrected pressure = Raw pressure + 3.08 (SD 0.33)

CTD temperatures were compared with calibrated digital reversing thermometer data. Excellent agreement was obtained with no evidence of drift or sudden offsets at any stage during the cruise. Consequently, no adjustment has been made to the CTD temperature data.


The CTD salinity data were calibrated against 8 (leg A) and 11 (leg B) water bottle samples analysed on a Guildline Autosal bench salinometer. The following corrections were obtained:

Leg A: Corrected salinity = Raw salinity + 0.042 (SD 0.008)
Leg B: Corrected salinity = Raw salinity + 0.029 (SD 0.006)

The fluorometer data were calibrated against extracted chlorophyll data assayed by HPLC, which were available for both legs of the cruise. Note that the data set supplied did not have chlorophyll-a resolved into normal and diavinyl forms.

Two fluorometers were deployed on the CTD during CD114. The instrument originally fitted (SA-254) was replaced by SA-234 after CTD60 on leg B, as the signal from SA-254 was extremely noisy. This can be seen in the calibrated chlorophyll data, especially at low chlorophyll concentrations.

The calibration strategy adopted was to calibrate each instrument rather than each leg, as there were insufficient data to calibrate the casts using SA-254 on leg B separately.

The calibrations obtained were:

SA-254: Chlorophyll (mg m-3) = 0.2572 * evoltage - 0.606 (N=129, R2=76%)
SA-234 Chlorophyll (mg m-3) = 1.0248 * evoltage - 1.3735 (N=72, R2=85%)
Optical Attenuance

There was a problem with the transmissometer calibration. No air readings were taken on the cruise and the only air readings on the instrument record sheet were taken in the laboratory using a voltmeter attached directly to the transmissometer. The value obtained (4.665 V) was virtually identical to the manufacturer's value (4.669 V).

No readings were available through the CTD electronics, and experience from other cruises has shown that these are significantly lower than direct measurements. The data were initially processed on the basis of the direct reading and the resulting attenuance values were obviously high.

Subsequent research revealed that the transmissometer had been used with the same CTD on a Discovery cruise immediately prior to CD114 for which air readings were available. The final reading from this cruise (4.580 V) was used to determine an attenuance correction of -0.092 per m. This has been applied to the data as a calibration.


The voltages logged by the ABC system from the SeaTech light backscatter sensor have been included in the database without the application of any further calibration.


There were problems with the dissolved oxygen data for both CD114A and B. Data logged during CTD upcasts were significantly lower and had opposite slopes to the data logged during the corresponding downcasts. An attempt was made to calibrate the downcast data against bottle data assayed by Winkler titration, but the relationship was extremely weak. Individual cast calibrations were then attempted, but the calibrated data made no sense when reviewed in conjunction with the chlorophyll data, which is hardly surprising considering the dramatic hysteresis observed. Consequently, the decision was taken to remove the dissolved oxygen data from the final data set.

Upwelling and Downwelling Irradiance

The following calibrations were applied to the voltages:

Downwelling irradiance (µEm-2s-1) = exp (-5.000*voltage + 6.536) * 0.0375
Sensor 11

Upwelling irradiance (µEm-2s-1) = exp (-4.970*voltage + 6.426) * 0.0375
Sensor 8

Note that the scaling factor (0.0375) is an empirically derived term that converts the data from µWcm-2 to µEm-2s-1. Consequently, the data may be converted to Wm-2 if required by dividing by 3.75.

Data Reduction

Once all screening and calibration procedures were completed, the data set was binned to 2 db (casts deeper than 100 db) or 1 db (casts shallower than 100 db). The binning algorithm excluded any data points flagged suspect and attempted linear interpolation over gaps up to 3 bins wide. If any gaps larger than this were encountered, the data in the gaps were set null.

Oxygen saturation has been computed using the algorithm of Benson and Krause (1984).


The chlorophyll data for casts CTD01-CTD60 are unusually noisy.


Benson B.B. and Krause D. jnr. 1984. The concentration and isotopic fractionation of oxygen dissolved in fresh water and sea water in equilibrium with the atmosphere. Limnol. Oceanogr. 29 pp.620-632.

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

Project Information

Ocean Margin EXchange (OMEX) II - II


OMEX was a European multidisciplinary oceanographic research project that studied and quantified the exchange processes of carbon and associated elements between the continental shelf of western Europe and the open Atlantic Ocean. The project ran in two phases known as OMEX I (1993-1996) and OMEX II - II (1997-2000), with a bridging phase OMEX II - I (1996-1997). The project was supported by the European Union under the second and third phases of its MArine Science and Technology Programme (MAST) through contracts MAS2-CT93-0069 and MAS3-CT97-0076. It was led by Professor Roland Wollast from Université Libre de Bruxelles, Belgium and involved more than 100 scientists from 10 European countries.

Scientific Objectives

The aim of the Ocean Margin EXchange (OMEX) project was to gain a better understanding of the physical, chemical and biological processes occurring at the ocean margins in order to quantify fluxes of energy and matter (carbon, nutrients and other trace elements) across this boundary. The research culminated in the development of quantitative budgets for the areas studied using an approach based on both field measurements and modeling.

OMEX II - II (1997-2000)

The second phase of OMEX concentrated exclusively on the Iberian Margin, although RV Belgica did make some measurements on La Chapelle Bank whilst on passage to Zeebrugge. This is a narrow-shelf environment, which contrasts sharply with the broad shelf adjacent to the Goban Spur. This phase of the project was also strongly multidisciplinary in approach, covering physics, chemistry, biology and geology.

There were a total of 33 OMEX II - II research cruises, plus 23 CPR tows, most of which were instrumented. Some of these cruises took place before the official project start date of June 1997.

Data Availability

Field data collected during OMEX II - II have been published by BODC as a CD-ROM product, entitled:

  • OMEX II Project Data Set (three discs)

Further descriptions of this product and order forms may be found on the BODC web site.

The data are also held in BODC's databases and subsets may be obtained by request from BODC.

Data Activity or Cruise Information


Cruise Name CD114A
Departure Date 1998-07-29
Arrival Date 1998-08-11
Principal Scientist(s)Ian Joint (Plymouth Marine Laboratory)
Ship RRS Charles Darwin

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
Q value below limit of quantification