Metadata Report for BODC Series Reference Number 1759751
Metadata Summary
Problem Reports
Data Access Policy
Narrative Documents
Project Information
Data Activity or Cruise Information
Fixed Station Information
BODC Quality Flags
SeaDataNet Quality Flags
Metadata Summary
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Problem Reports
Problem report
All underway salinity data should be treated with caution due to pump problems.
The salinity channel is subject to problems with bubbles or reduced flow rate at times when the ship was hove-to on station. Where the effect is clear, the parameter has been flagged. Salinity is obviously degraded, but it is not possible to tell which values are suspect and which, if any, are reliable.
Sea surface hydrography data were screened with reference to NMF-SS technical reports, and to the navigation data, to help diagnose episodes of bubbling or impaired flow rate.
Salinity data were calibrated from 26/05/2012 04:34 to 14/06/2012 18:00 due to data quality concerns with the Thermosalinograph (TSG) channel from earlier in the cruise, therefore salinity should be used with caution.
UK Ocean Acidification RRS James Cook Cruise JC073 Underway Surface Hydrography Data Quality Report
Salinity, transmittance, attenuance and fluorescence channels were significantly affected by problems with the pumped surface supply as described in NMF Ship Systems report. For a large period of the cruise, the ship was hove to on station and compromised the flow through the pumped system causing bubbling and reduced flow-rate, which resulted in data quality issues.
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
SeaBird Digital Oceanographic Thermometer SBE38
The SBE38 is an ultra-stable thermistor that can be integrated as a remote temperature sensor with an SBE21 Thermosalinograph or an SBE 45 Micro TSG, or as a secondary temperature sensor with an SBE 16 plus, 16plus-IM, 16plus V2, 16plus-IM V2 or 19plus V2 SEACAT CTD.
Temperature is determined by applying an AC excitation to reference resistances and an ultra-stable aged thermistor. The reference resistor is a hermetically sealed VISHAY. AC excitation and ratiometric comparison using a common processing channel removes measurement errors due to parasitic thermocouples, offset voltages, leakage currents and gain errors.
The SBE38 can operate in polled sampling, where it takes one sample and transmits the data, or in continuous sampling.
Specifications
| Depth rating | up to 10500 m |
| Temperature range | -5 to 35°C |
| Initial accuracy | ± 0.001°C |
| Resolution | 0.00025°C |
| Stability | 0.001°C in 6 months |
| Response time | 500 ms |
| Self-heating error | < 200 µK |
Further details can be found in the manufacturer's specification sheet.
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.
Specifications
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.
WETLabs C-Star transmissometer
This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.
Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.
This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.
Specifications
| Pathlength | 10 or 25 cm |
| Wavelength | 370, 470, 530 or 660 nm |
| Bandwidth | ~ 20 nm for wavelengths of 470, 530 and 660 nm ~ 10 to 12 nm for a wavelength of 370 nm |
| Temperature error | 0.02 % full scale °C-1 |
| Temperature range | 0 to 30°C |
| Rated depth | 600 m (plastic housing) 6000 m (aluminum housing) |
Further details are available in the manufacturer's specification sheet or user guide.
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:
- Polled sampling: the instrument takes one sample on command
- Autonomous sampling: the instrument samples at preprogrammed intervals and does not enter quiescence (sleep) state between samples
- Serial Line Sync: a pulse on the serial line causes the instrument to wake up, sample and re-enter quiescent state automatically
Specifications
| 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.
UK Ocean Acidification RRS James Cook Cruise JC073 Underway Surface Hydrography Instrumentation
The instruments used to collect the surface hydrography datasets are displayed in the table below.
| Sensor | Serial number | Last calibration date |
|---|---|---|
| Sea-Bird SBE38 | 3853440-0416 | 2011-06-27 |
| Sea-Bird SBE45 | 4548881-0230 | 2011-09-03 |
| Wetlabs C-Star | CST-1132PR | 2011-07-05 |
| Wetlabs WetStar | WS3S-246 | 2011-08-09 |
UK Ocean Acidification RRS James Cook Cruise JC073 Underway Surface Hydrography Data Processing Document
Originator's Data Processing
During the cruise there was a dual logging system in place on the RRS James Cook. Data from the various instruments were logged to the RVS Level-C system and also as NetCDF (binary) through the Ifremer Techsas data logging system. Processing was carried out using the RVS software suite.
Sea surface temperature was measured in situ, with a temperature probe mounted at 5 m depth on the ship's hull. Other hydrographic parameters were measured by instruments supplied by a pumped seawater system, with its intake co-located with the in situ temperature probe.
BODC Data Processing
Reformatting
The underway data were reformatted from the originator's ASCII format to BODC's in-house standard. All parameters were merged into a single file, with a common time channel. Data supplied at higher frequency than the BODC file were bin-averaged to the appropriate time-interval.
The following sea surface hydrography parameters were transferred to the BODC underway file:
| Channels | Description | Units | BODC Parameter Code | Units | Conversion Factor |
|---|---|---|---|---|---|
| temp_h | TSG housing temperature | Degrees Celsius | TMESSG01 | Degrees Celsius | - |
| temp_r | Remote temperature at non-toxic inlet | Degrees Celsius | TEMPHU01 | Degrees Celsius | - |
| cond | TSG conductivity | S m-1 | CNDCSG01 | S m-1 | - |
| fluo | Raw fluorometer voltage | V | FVLTWS01 | V | - |
| trans | Raw transmissometer voltage | V | TVLTDR01 | V | - |
Screening
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.
Manufacturers Calibrations
Transmittance and attenuance
BODC applied the manufacturers' instrument calibrations to the transmissometer voltage data:
| Parameter | Equation | Date of calibration | Comments |
|---|---|---|---|
| Beam transmittance | POPTDR01 = TVLTDR01 x 21.645020 - 1.277056 | 25/07/2011 | - |
| Beam attenuation | ATTNDR01 = -4 x ln(POPTDR01 x 0.01) | n/a | - |
Field Calibrations
BODC derived calibrations for the hull sensor temperature sensor and TSG salinity measurements from CTD data from 5-7m depth:
Temperature
| Parameter | Equation | BODC ICALRF | Comments |
|---|---|---|---|
| Hull temperature | TEMPHG01 = TEMPHU01 - 0.0521 | 7036 | - |
| TSG salinity | PSALSG01 = PSALSU01 with a linear offset applied of value -0.0080 at 26/05/2012 04:34 and +0.0058 at 14/06/2012 18:00. | 7056 | Only applied for period 26/05/2012 04:34 to 14/06/2012 18:00 due to data quality concerns with the TSG daa from earlier in the cruise. |
Salinity
The salinity sensor drifted over time, so a calibration was generated that applies the appropraite offset at the start and end of the phase was applied. A calibration was only applied for the period 26/05/2012 04:34 to 14/06/2012 18:00 due to data quality concerns with the TSG data from earlier in the cruise.
Offset at 26/05/2012 04:34 = - 0.0080
Offset at 14/06/2012 18:00 = + 0.0058
Project Information
UKOARP Theme B: Ocean acidification impacts on sea surface biology, biogeochemistry and climate
The overall aim of this theme is to obtain a quantitative understanding of the impact of ocean acidification (OA) on the surface ocean biology and ecosystem and on the role of the surface ocean within the overall Earth System.
The aims of the theme are:
- To ascertain the impact of OA on planktonic organisms (in terms of physiological impacts, morphology, population abundances and community composition).
- To quantify the impacts of OA on biogeochemical processes affecting the ocean carbon cycle (both directly and indirectly, such as via availability of bio-limiting nutrients).
- To quantify the impacts of OA on the air-sea flux of climate active gases (DMS and N2O in particular).
The main consortium activities will consist of in-situ measurements on three dedicated cruises, as well as on-deck bioassay experiments probing the response of the in-situ community to elevated CO2. Most of the planned work will be carried out on the three cruises to locations with strong gradients in seawater carbon chemistry and pH; the Arctic Ocean, around the British Isles and the Southern Ocean.
Weblink: http://www.oceanacidification.org.uk/research_programme/surface_ocean.aspx
Data Activity or Cruise Information
Cruise
| Cruise Name | JC073 |
| Departure Date | 2012-05-18 |
| Arrival Date | 2012-06-15 |
| Principal Scientist(s) | John Murray Roberts (Heriot Watt University School of Life Sciences) |
| Ship | RRS James Cook |
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 |
