Metadata Report for BODC Series Reference Number 1359851
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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Parameters |
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Problem Reports
No Problem Report Found in the Database
RRS James Clark Ross Cruise AMT14 (JR20040428) - Underway Hydrography Data Quality Report
A few periods during the dataset and a few spikes considered suspect were flagged 'M'.
PSALSGU01 data below the Limit for detection of the parameter have been flagged as Null. These data occurred at the start of the dataset till 19:45:00 28/04/2004.
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
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.
Trimble 4000DS Global Positioning System receiver
The Trimble 4000DS Differential Surveyor is similar to the 4000RS (a Maxwell-based receiver that is oriented toward precision positioning applications. It is intended for use as a DGPS base station, generating RTCM-104 corrections). The 4000Ds can apply RTCM-104 corrections to the satellite data it receives in order to generate accurate position fixes in real time.
RRS James Clark Ross Cruise AMT14 (JR20040428) - Underway Hydrography Instrumentation Document
The following instruments were used to obtain hydrographic measurements:
| Manufacturer | Model | Main Function | Serial Number | Comments |
|---|---|---|---|---|
| Trimble | 4000DS | Position (Latitude and Longitude) | - | - |
| Turner Instruments | 10AU | Fluorometer | 005-CE | - |
| SeaBird | SBE45 | Salinity | - | Conductivity 0 - 7 S m-1 |
| Temperature | - | -5 - 35°C |
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 AMT14 (JR20040428) - Underway Hydrography Processing Document
Originator's Data Processing
The raw data were logged every second to the SCS logging system. The latitude and longitude navigation data originated from the Trimble 4000DS Trimble Surveyor system using Marine Star differential corrections.
The data were submitted to BODC in ASCII output from the BAS SCS system for post-cruise processing and data banking.
BODC Data Processing
Reformatting
Data from the full-resolution SCS files were transferred to BODC's NetCDF format QXF under the BODC Underway Data System (BUDS). The transfer involved reducing the data to 60 second intervals.
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.
Values that were outside the parameters designated limits for detection were flagged 'M'.
Data processing, correction and calibration
Navigational data were available from three different systems on the JCR. These were screened in order to select the best quality data for the primary navigation channels. The data from the Trimble GPS system were consistently good and showed no spikes.
A program was run which located any null values in the latitude and longitude channels and checked to ensure that the ship's speed did not exceed 15 knots. There was 1 speed check failures in the Trimble navigation data and 2 small gaps. These points were screened again to look for improbable spikes which were flagged as null. The gaps were then filled using linear interpolation.
Temperature
TSG temperature was checked against the CTD temperature measurements averaged over the upper 6 m of the water column. Only CTD data points with a standard deviation (SD)< 0.01 °C in the upper 6 m and underway records with SD< 0.01°C over the duration of the cast were considered. Based on a total of 23 paired samples, the diffference between the TSG and the CTD values averaged 0.00 degree C ±0.03 and ranged between -0.08 and 0.05°C with no obvious trend. No correction was applied to the TSG channel.
Salinity
Salinity data from the thermosalinograph have been compared with calibrated surface CTD data to a depth of 20 m. This is usually done to a depth of 6 m, however, the CTD data down to 6 m depth are suspect. There was no time information for water samples so used calibrated CTD to calibrate the underway salinity. However, there were no data for CTD salinity down to 6 m depth - the value usually used in the function 'intcal' to average the CTD salinities. Different averaging depths (6 m, 10 m, 15 m and 20 m) were investigated and it was found that it was needed to average 20 m of CTD salinity data. Comparison of all depth averages to the underway data shows that there is no adverse effect in increasing the depth averaging window to 20 m. It was therefore decided to calibrate the underway salinity data to the calibrated CTD data averaged over 20 m depth. The underway data were averaged over the period of CTD deployments and standard deviations were used to check the quality of the data. The 84 samples showed the following relationship, which has been used to produce a calibrated temperature channel (PSALSG01).
PSALSG01 = 0.994056 * PSALSU01 + 0.225660 (BODC calibration reference 3796)
Chlorophyll-a
The fluorometer channel was calibrated by comparing the uncalibrated fluorometer output with chlorophyll concentration values extracted from samples collected from the ship's non-toxic water supply (N=263). The relationship between extracted and fluorometer values was reasonable (R2=0.76) and apparently unskewed.
The following equation was derived by linear regression:
CPHLUT01 = 1.861 (±0.065) * CPHLUMTF - 0.098 (±0.012), R2=0.76
Residuals (extracted chlorophyll from the non-toxic minus calibrated fluorometer) follow a normal distribution and range between -0.73 and 0.53 mg chl m-3 for chlorophyll concentrations ranging from 0.09 to 1.48 mg Chla m-3. The largest variations are due to a peak in the chlorophyll concentration values around 16/05/2004 which is not present in the fluorometer readings.
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
| Cruise Name | JR20040428 (AMT14, JR101) |
| Departure Date | 2004-04-28 |
| Arrival Date | 2004-06-01 |
| Principal Scientist(s) | Patrick M Holligan (University of Southampton School of Ocean and Earth Science) |
| 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 |
