Metadata Report for BODC Series Reference Number 1762212
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
Data Description |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Data Identifiers |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time Co-ordinates(UT) |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spatial Co-ordinates | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Parameters |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Problem Reports
No Problem Report Found in the Database
AMT RRS James Cook Cruise JC053 AMT20 Surface Hydrography Data Quality Document
The underway log sheets were used as a guide to the times when the non-toxic flow was switched off, dropped low or was adjusted during the cruise. Where there was noise in the channel at these times the data were flagged suspect. If there was no noise or spiking the data remain unflagged.
The sample calibrations applied to the TSG salinity and hull sensor temperature channels appear reasonable and did not produce suspect data in the calibrated channels.
Fluorometer
During the cruise concern was raised at the fluorometer's lack of response to low magnitude changes that had been observed in the discrete surface underway samples as the track crossed the equatorial upwelling waters (voltage level ~ 0.11 volts in open ocean gyre waters and no increase through the upwelling waters where discrete sample concentrations increased from <0.1 mg m-3 to 0.2-0.3 mg m-3). While data collection was stopped during the visit to Ascension Island on 8th November 2010, testing and cleaning of the transmissometer and fluorometer were carried out. Cleaning the fluorometer had little impact on the readings with MilliQ water (~0.14 volts before and after cleaning). At this stage it was noted that the fluorometer tubing was clear and possibly letting light into the sensor, affecting sensitivity for low level readings. Black tape was then added to the outlet tube of the fluorometer to prevent external light from entering the instrument. After the addition of the tape the voltage returned with MilliQ water passing through the sensor matched the calibration sheet value for MilliQ water (0.081 volts). All fluorometer data prior to this time may have been affected by this light pollution.
The calibrated fluorometer data exhibit large amounts of variability towards the end of the cruise in the southern Atlantic Ocean. The calibration in this area is not as closely matched to the sample data for this reason and for a few small periods the calibration results in values less than zero, which have been flagged suspect. Users should keep this in mind when using the sample calibrated fluorometer data.
Attenuance and transmittance
For the first few days there was noise in the transmissometer data that started whenever the ship stopped on station for a CTD cast. Initially there was concern that this was due to a fault with the equipment and the transmissometer was stopped briefly at 11:35 on 18th October to replace instrument CST-1132PR with CST-1131PR. The problems continued and it was realized that bubbles were becoming trapped in the transmissometer. Logging was stopped again between 10:27 and 11:35 on 20th October; CST-1132PR was inserted again (since the calibration for sensor CST-1131PR was found to be out of date) and the plumbing set up was changed so that it remained mounted vertically but with water entering at the bottom of the transmission tube and leaving at the top, in the hope that any bubbles would travel out of the top of the transmission tube with the water exiting it. This was successful and noise was not seen again in the instrument.
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.
AMT RRS James Cook Cruise JC053 AMT20 Surface Hydrography Instrument Description Document
| Sensor | Serial number | Last calibration date | Deployment |
| Sea-Bird SBE38 | 0416 | 2010-03-15 | Hull inlet to non-toxic supply |
| Sea-Bird SBE45 | 0233 | 2010-03-18 | CTD hanger non-toxic supply |
| Wetlabs C-Star | CST-1132PR | 2010-06-04 | CTD hanger non-toxic supply up to 2010-10-18 11:35 from 2010-10-20 11:35 |
| Wetlabs C-Star | CST-1131PR | 2008-07-15 | CTD hanger non-toxic supply 2010-10-18 11:35 - 2010-10-20 11:35 |
| Wetlabs WetStar | WS3S-246 | 2010-06-30 | CTD hanger non-toxic supply |
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.
AMT RRS James Cook Cruise JC053 AMT20 Surface Hydrography Processing Procedures Document
Originator's Data Processing
The surface water component consisted of a flow through system with a pumped pickup at approx 5 m depth. TSG flow was approx 18 litres per minute whilst fluorometer and transmissometer flow is approx 1.5 litres per minute. Flow to instruments is degassed using a debubbler with 24 litres per minute inflow and 10 litres per minute waste flow. The non-toxic system ran throughout the cruise except when entering within 200 nautical miles of the Azores , Ascension Island, Falklands and Argentina.
The data from the non-toxic supply were logged by the TECHSAS system during the cruise and combined in RVS Level-C format to produce the files 'surfmet' and 'sbe45'. The following instruments were logged during the cruise:
1) Wetlabs C-star 25 cm pathlength transmissometer (logged to RVS format in surfmet)
2) Wetlabs WetStar fluorometer (logged to RVS format in surfmet)
3) Seabird SBE38 Temperature sensor (logged to RVS format in sbe45)
4) Seabird SBE45 MicroTSG (logged to RVS format in sbe45)
| Filename | Data type | Start Calendar Day | Start Time | Finish Calendar Day | Finish Time | Interval |
| sbe45 | RVS Level-C raw | 2010-10-12 | 12:22:38 | 2010-11-22 | 21:10:09 | 1 second |
| surfmet | RVS Level-C raw | 2010-10-12 | 07:50:36 | 2010-11-22 | 21:10:09 | 1 second |
BODC Data Processing
The 'surfmet' and 'sbe45' files were used as the source data for transfer. A description of the channels present in the files, units, whether they were transferred, BODC parameter code and units, and if a unit conversion was applied during the transfer are detailed in the table below:
| surfmet | Channels | Description | Units | BODC Parameter Code | Units | Conversion Factor |
| temp_h | TSG housing temperature | - | not for transfer - channel null in file | - | - | |
| temp_m | Remote temperature at non-toxic inlet | - | not for transfer - channel null in file | - | - | |
| cond | TSG conductivity | - | not for transfer - channel null in file | - | - | |
| fluo | Raw fluorometer voltage | V | FVLTWS01 | V | *1 | |
| trans | Raw transmissometer voltage | V | TVLTDR01 | V | *1 | |
| sbe45 | Channels | Description | Units | BODC Parameter Code | Units | Conversion Factor |
| temp_h | TSG housing temperature | Degrees Celsius | TMESSG01 | Degrees Celsius | *1 | |
| cond | TSG conductivity | S m-1 | CNDCSG01 | S m-1 | *1 | |
| salin | Salinity | PSU | PSALSU01 | dimensionless | *1 | |
| sndspeed | Velocity of sound in water | m s-1 | SVELSG01 | m s-1 | *1 | |
| temp_r | Remote temperature at non-toxic inlet | Degrees Celsius | TEMPHU01 | Degrees Celsius | *1 |
Calibrations
Transmissometer - conversion from voltage using manufacturer's calibrations
The coefficients from the calibration sheets provided for each transmissometer were used to generate the calibration equation to convert the raw voltage to transmittance and then to attenuance.
Temperature
The hull temperature sensor data were calibrated against the CTD profile temperature. The data from the hull sensor at the CTD start time were compared with the temperature from the CTD averaged over the surface 5 decibars. The temperature offsets (CTD - Hull) were plotted against date/time and CTD sensor temperature and outliers identified and removed from the calibration dataset. The relationships in the offset between sensors were then compared to the date/time and the CTD sensor temperature in separate linear regressions. There was no significant relationship with CTD sensor temperature (R2 = 0.003; n = 74; F = 0.184; p = 0.669). There was a significant regression of offset with date/time (R2 = 0.117; n = 74; F = 9.502; p = 0.003).
Applying the significant regression equation the offset was generated at the date/time when the non-toxic underway system was switched on (13/10/2010 07:00 offset = -0.0012) and when switched off at the end of the cruise (22/11/2010 21:05 offset = -0.0087). The offset was applied for the period in-between by linear interpolation of these offsets through the BODC BUDS calibration routine (BODC ICALRF 6581).
Salinity
The SBE45 salinity data were calibrated against bench salinometer data from samples collected from the underway system during the cruise. The data from the SBE45 TSG at the discrete sampling times were compared with the bench salinometer measurements. The salinity offsets (bench - TSG) were plotted against date/time and bench salinity and outliers identified. The relationships in the offset between TSG and bench salinometer were then compared to the date/time and the bench salinity in separate linear regressions. There was a significant relationship of offset with date/time (R2 = 0.055; n = 159; F = 9.157; p = 0.003) but not bench salinity (R2 = 0.006; n = 159; F = 0.950; p = 0.331).
Applying the significant equation from the date/time regression, the offset was generated at the date/time when the non-toxic underway system was switched on (13/10/2010 07:00 offset = 0.012) and when switched off at the end of the cruise (22/11/2010 21:05 offset = 0.003). The offset was applied for the period in-between by linear interpolation of these offsets through the BODC BUDS calibration routine (BODC ICALRF 6503).
Fluorescence
The fluorometer voltage data were calibrated against extracted chlorophyll-a data from samples collected from the underway system during the cruise. Samples of seawater collected and extracted chlorophyll-a measurements made following Welschmeyer (1994). Each 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 then analysed on a pre-calibrated Turner Designs Trilogy fluorometer with a non-acidified chl module (CHL NA #046) fitted. The bench fluorometer calibration was checked against dilutions of pure chlorophyll stock during the cruise and no modifications to the calibration were necessary.
The raw voltage data from the fluorometer at the discrete sampling times were converted to nominal chl-a concentrations based on the manufacturer's calibration and these values were compared with the extracted chlorophyll-a measurements. The offsets (extracted chl-a - nominal chl-a) were plotted against date/time and extracted chlorophyll-a and outliers identified. Based on a preliminary calibration against extracted chl-a, which over stated the chlorophyll concentrations at the start of the cruise; it was decided to split the dataset for calibration. The calibration dataset was split into a number of sections to correct for different periods of drift in the sensor. These changes were related to different sections of the cruise where the non-toxic system had been turned off/on and/or cleaned.
| Start | End | Calibration | N | R2 | BODC ICALRF |
|---|---|---|---|---|---|
| 13/10/2010 07:00 | 19/10/2010 21:22 | CPHLUT01 = 0.1468 *CPHLUMTF + 0.0385 | 22 | 0.747 | 6514 |
| 19/10/2010 21:22 | 23/10/2010 15:00 | Start offset = -0.3577 End offset = -0.1648 | 11 | 0.519 | 6516 |
| 23/10/2010 15:00 | 27/10/2010 00:55 | Start offset = -0.1926 End offset = -0.3594 | 17 | 0.515 | 6517 |
| 27/10/2010 00:55 | 04/11/2010 10:00 | Start offset = -0.1291 End offset = -0.3135 | 20 | 0.408 | 6518 |
| 04/11/2010 10:00 | 08/11/2010 07:30 | Start offset = -0.1681 End offset = -0.5024 | 14 | 0.717 | 6519 |
| 08/11/2010 15:58 | 17/11/2010 19:00 | Start offset = -0.0391 End offset = -0.1248 | 33 | 0.253 | 6520 |
| 17/11/2010 19:00 | 22/11/2010 21:05 | CPHLUT01 = 0.4124 *CPHLUMTF - 0.2878 | 16 | 0.790 | 6515 |
Screening
Each data channel was inspected on a graphics workstation using BODC screening software EDSERPLO and any spikes or periods of dubious data were flagged using BODC quality control flag system. Impossible values were checked carefully and flagged null only if believed to be genuine missing or bad data. EDSERPLO 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.
References
Welschmeyer N.A., 1994. Fluorometric analysis of chlorophyll-a in the presence of chlorophyll-b and phaeopigments. Limnology and Oceanography, 39:1985-1992.
Project Information
Oceans 2025 Theme 10, Sustained Observation Activity 1: The Atlantic Meridional Transect (AMT)
The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.
The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:
- give early warning of any fundamental change in Atlantic ecosystem functionng
- improve forecasts of the future ocean state and associated socio-economic impacts
- provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.
The specific objectives are:
- To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands
- To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems
- To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases
The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).
More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10
Weblink: http://www.oceans2025.org/
Data Activity or Cruise Information
Cruise
| Cruise Name | JC053 (AMT20) |
| Departure Date | 2010-10-12 |
| Arrival Date | 2010-11-25 |
| Principal Scientist(s) | Andrew Rees (Plymouth Marine Laboratory) |
| 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 |
