Metadata Report for BODC Series Reference Number 1762389
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
Fluorescence
The underway fluorometer may be operating close to the lower limits of detection for the instrument along much of the transect. The bench fluorometric measurements made on discrete samples collected for the extraction of chlorophyll-a recorded marked difference between different regions of the cruise track whereas the underway fluorometer shows continuously similar values from around 24/10/2015. Data from this point onwards have been flagged. The fluorometer readings show jumps in values throughout the cruise. There is no record of the fluorometer being cleaned before or during the cruise and the observed pattern may be due to bio-fouling of the sensor further reducing the limits of detection. For this reason the discrete underway chlorophyll-a measurement data sets should be used in preference to the ship's fluorometer.
RRS James Clark Ross Cruise JR15001 (AMT25, JR864) Surface Hydrography Data Quality Report
Salinity, Temperature, Conductivity and Sound velocity
Unrealistic values in the PSALSU01, TEMPHU02, TEMPHU01, SVELSG01 and CNDCSG01 channels were flagged as suspect.
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.
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.
Specifications
| 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.
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.
Litre Meter flow meter
A flow meter used to monitor water flow rates for pumped systems such as ships' continuous seawater supplies.
RRS James Clark Ross Cruise JR15001 (AMT25, JR864) Surface Hydrography Instrument Description Document
The following instruments were used during the cruise.
Instrumentation
| Manufacturer | Model | Main Function | Serial number | Last calibration date |
| Sea Bird Electronics | SBE45 | Thermosalinograph | 0016 | 14/05/2014 |
| Sea Bird Electronics | SBE38 | Temperature x2 sensors | 0601 and 0599 | 11/06/2015 |
| Chelsea Technologies | 10 AU-005 | Fluorometer | 1100243 | - |
| Wet Labs | C-Star | Transmissometer | CST-396DR | 06/08/2015 |
| Litremeter | 05SPFA40CE | Flow meter | 05/811950 | 09/06/2011 |
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.
RRS James Clark Ross Cruise JR15001 (AMT25, JR864) Surface Hydrography Processing Document
Originator's Data Processing
The sea surface hydrography measurements were performed by a Sea Bird electronics thermosalinograph in the ship's flow through system and by a temperature sensor located near the flow through intake, at the hull. The depth of the flow through intake was 5.5 m. The data streams were logged every second to the SCS system and merged into a comma separated file format, and the header information was stored in .TPL files.
The surface hydrography data were also logged to the Oceanlogger.ACO file. This file exhibits four initial columns: Year (yyyy), Julian day.day fraction (days), Julian day (days), day fraction (days). The file structure then contains 10 columns with meteorological data as outlined above followed by the hydrography channels in the order: tstemp (Celsius), conductivity (S m-1), salinity (psu), sound_velocity (m s-1) chlorophyll (µg l-1), sampletemp (Celsius), flowrate (l min-1), sstemp (Celsius).
| Filename | Content Description | Format | Interval | Start date | Start Time | End date | End Time |
| oceanlogger.ACO |
| ASCII (.ACO) | ~1-2 minutes | 15/9/2015 | 14:18:00 | 04/11/2015 | 14:50:40 |
BODC Data Processing
Sea surface hydrography parameters were transferred to internal BODC format and matched against BODC parameter codes, as presented in the table below. No unit conversions were applied, as the originators units were equivalent to the units of the respective BODC parameter code units assigned. BODC processing procedures included loading of data and reduction through averaging, unit conversions, visual screening and flagging of anomalous values.
| Originator's File | Originator's Parameter | Originator's Units | Description | BODC code | BODC Units | Comments and unit conversions |
|---|---|---|---|---|---|---|
| oceanlogger.ACO | salinity | psu | Practical salinity of the water body by thermosalinograph and computation using UNESCO 1983 algorithm and NO calibration against independent measurements | PSALSU01 | Dimensionless | - |
| oceanlogger.ACO | sstemp | °C | Temperature of the water body by thermosalinograph hull sensor and NO verification against independent measurements | TEMPHU01 | °C | - |
| oceanlogger.ACO | sstemp2 | °C | Temperature of the water body by thermosalinograph hull sensor and NO verification against independent measurements sensor 2 | TEMPHU02 | °C | - |
| oceanlogger.ACO | tstemp | °C | Temperature of conductivity measurement by thermosalinograph | TMESSG01 | °C | - |
| oceanlogger.ACO | conductivity | S m-1 | Electrical conductivity of the water body by thermosalinograph | CNDCSG01 | S m-1 | - |
| oceanlogger.ACO | sound_velocity | m s-1 | Sound velocity in the water body by thermosalinograph and computation from temperature and salinity by unspecified algorithm | SVELSG01 | m s-1 | - |
| oceanlogger.ACO | chlorophyll | µg l-1 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate phase] by through-flow fluorometer plumbed into non-toxic supply and manufacturer's calibration applied | CPHLUMTF | mg m-3 | - |
| oceanlogger.ACO | flowrate | l min-1 | Flow rate through instrument | INFLTF01 | l min-1 | - |
| oceanlogger.ACO | trans | % | Transmittance | POPTDR01 | % | x 100 % |
Sample Calibrations
Temperature
The hull temperature sensor data were calibrated against the CTD temperature sensors during the cruise. The data from the hull sensor were compared with the temperature from the average of two externally mounted CTD temperature sensors at 6 decibars at corresponding measurement times. The temperature offsets (CTD - Hull) were plotted against cruise day and CTD sensor temperature to identify and remove outliers. A regression analysis was run on the remaining data points and revealed a weak and insignificant relationship between the offset and CTD sensor data (R2= 0.0458; n = 58; p = 0.1066) and between the offset and cruise time (R2 = 0.047; n = 58; p = 0.099). The mean offset was therefore applied to the uncalibrated hull temperature data.
The mean offset was applied to the hull mounted temperature sensor as shown in the equation below to generate the calibrated hull temperature channel.
- BODC ICALRF 7816, TEMPHG01 = TEMPHU01 - 0.01203
Salinity
Bench salinometer discrete surface samples collected from the non-toxic underway system during the cruise were used to create a calibration dataset for the calibration of the SBE45 TSG salinity data. The offset between the bench salinity and TSG salinity was calculated and plotted against bench salinity to identify outliers. The relationship between the offset and time was also assessed to check for any drift in the sensor over the course of the cruise and to remove further outliers. Two phases over the duration of the cruise were identified and required two separate analyses. The first phase was from the start of the cruise to the port dock at Cape Verde at 07/10/2015 20:59, and the second phase was from 07/10/2015 21:00 to the end of the cruise. The relationship between the offset and bench salinity and between offset and cruise day were then analysed using a linear regression for each phase.
In the first phase, the relationship between offset and cruise time, although not strong, was significant (R2 = 0.191; n = 37; p = 0.0068), indicating a possible sensor drift over time. However, the quality of the bench salinity measurements were in question for the first half of the cruise and therefore applying a calibration was not deemed appropriate.
For the second phase of the cruise, the sensor drift over time was not strong or significant (R2 = 0.018; n = 56; p = 0.325). As the relationship between offset and bench salinity (R2 = 0.00005; n = 56; p = 0.957) for this phase was also weak and insignificant a regression was not applied. The TSG salinity is only reported to 2 decimal places and the mean offset in the second half of the cruise was less than +/-0.01 so that applying a mean offset did not move the TSG values closer to the bench salinity, so therefore a calibration was not necessary to improve the dataset.
Chlorophyll
Discrete samples of seawater were collected during the cruise from the non-toxic supply and analysed for extracted chlorophyll-a following Welschmeyer (1994). These samples were obtained to create a calibration dataset for the underway fluorometer sensor. Each discrete sample of 250 ml was filtered through a 47 mm 0.2 µm polycarbonate filter. The filters were then placed in a vial with 10 ml 90% acetone and left in a freezer for 24 hours. The samples were analysed on a pre-calibrated Turner Designs Trilogy fluorometer with a non-acidified chl module (CHL NA #046) fitted.
The underway fluorometer readings appear to be unrealistic, displaying values that flat-line from around the 24/10/2015 onwards. As a result of this, no calibration has been applied to the fluorometer channel.
Project Information
No Project Information held for the Series
Data Activity or Cruise Information
Cruise
| Cruise Name | JR15001 (AMT25, JR864) |
| Departure Date | 2015-09-15 |
| Arrival Date | 2015-11-04 |
| Principal Scientist(s) | David Barnes (British Antarctic Survey), Jonathan Sharples (University of Liverpool Department of Earth, Ocean and Ecological Sciences), Tim Smyth (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 |
| B | nominal value |
| Q | value below limit of quantification |
