Metadata Report for BODC Series Reference Number 2219311
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
No Problem Report Found in the Database
RRS James Cook cruise JC071 sea surface hydrography quality control report
Pumped sea water flow
All sensors were affected at the start of the series when the non-toxic pump did not appear to be switched on (29/4/2012 09:27:00 to ~20:15:00). All sensors appeared to be suspect towards the end of the series when it is likely the non-toxic supply was switched off. Data were flagged suspect from 11/05/2012 20:20:30. (BODC assessment)
Trapped bubbles
All sensors (except the hull temperature sensor) appeared to be affected by a bubble in the water sampling laboratory between the 30/4/2012 and 01/05/2012 as reported by the NMF technicians on board. Data were flagged suspect from ~30/4/2012 07:51:00 to ~01/05/2012 08:25:00 where data were clearly affected. (BODC and originator's assessment)
Sensors in the SBE 45 TSG were affected by a trapped bubble between the 3/5/2013 02:42:00 - 08:30:00 as reported by the NMF technicians on board. Data were flagged suspect over this period. (Originator's assessment)
Data Access Policy
Open Data
These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.
If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:
"Contains public sector information licensed under the Open Government Licence v1.0."
Narrative Documents
RRS James Cook Cruise JC071 underway document
Cruise details
| Dates | 29th April 2012 - 12th May 2012 (UTC) |
|---|---|
| Principal Scientific Officer | Richard Lampitt (National Oceanography Centre) |
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.
RRS James Cook Cruise JC071 surface hydrography instrumentation
Instrumentation
The sea surface hydrographical suite of sensors was fed by the pumped-seawater, non-toxic supply. The seawater intake was located approximately 5.5 m below the sea surface. The SBE38 temperature sensor was located towards the hull near the seawater intake. All other sensors were located further towards the interior of the ship, primarily in the water sampling laboratory. The pumped sea water flow rate was approximately 1500 ml min-1.
| Manufacturer | Model | Serial no. | Last Manufacturer's Calibration Date | Comments |
| Wet Labs Fluorometer | WETStar | WS3S-246 | 09/08/2011 | |
| Wet Labs Transmissometer | CST | CST-1132PR | 25/07/2011 | 25 cm, 660 nm |
| Sea-Bird Temperature sensor | SBE38 | 3853440-0416 | 27/06/2011 | Hull |
| Sea-Bird Thermosalinograph | SBE45 | 4548881-0233 | 19/07/2011 |
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 Cook cruise JC071 surface hydrography data processing procedures
Originator's Data Processing
All underway sensors/instruments were initially logged via the Ifremer TECHSAS (TECHnical and Scientific sensors Acquisition System) system. The data were then broadcast in UDP/IP frames via the on-board LAN. Data were broadcast in two formats: NMEA broadcasting format and XML broadcasting format. The XML broadcast was used to create TECHSAS NetCDF files while the NMEA broadcast was used to transfer data to the RVS Level-C UNIX system where it was parsed into RVS data streams (RVS format files). Data were not further processed in Level-C on JC071. For more information please see the JC071 cruise report.
Files delivered to BODC
| Filename | Content description | Format | Interval | Start date/time (UTC) | End date/time (UTC) | Comments |
| sbe45 | TSG | UKORS | 1 Hz | 29/04/2012 09:26 | 11/05/2012 20:59 | TSG not delayed in time |
| surfmet | Sea surface hydrography | UKORS | 1 Hz | 29/04/2012 09:26 | 11/05/2012 20:59 | Sea surface hydrography |
BODC Data Processing
sbe45 and surfmet were selected for transfer into BODC format since they contained the most processed sea surface hydrography data. The TSG data (salinity, temperature and conductivity) were sourced from the sbe45 data stream since the same variables in surfmet may be delayed in time. The data was reformatted to NetCDF using BODC standard data banking procedures. The following table shows how variables within the file were mapped to appropriate BODC parameter codes:
sbe45
| Originator's variable | Originator's units | Description | BODC Code | BODC Units | Unit conversion | Comments |
| Time | date | Year Julian day time | ||||
| temp_h | deg C | TSG housing temperature | TMESSG01 | deg C | ||
| cond | S m-1 | Conductivity | CNDCSG01 | S m-1 | ||
| salin | dimensionless | Practical salinity | PSALSU01 | dimensionless | ||
| sndspeed | m s-1 | Sound velocity | Derived | |||
| temp_r | deg C | Sea surface temperature | TEMPHU01 | deg C |
surfmet
| Originator's variable | Originator's units | Description | BODC Code | BODC Units | Unit conversion | Comments |
| Time | date | Year, Julian, day time | ||||
| temp_h | deg C | TSG housing temperature | Not preferred source | |||
| temp_r | deg C | Sea surface temperature | Not preferred source | |||
| cond | S m-1 | Conductivity | Not preferred source | |||
| fluo | volt | Raw fluorometer output | FVLTWS01 | volts | ||
| trans | volt | Raw transmissometer output | TVLTDR01 | volts | ||
| press | hPa | Air pressure | ||||
| ppar | volt x105 | PAR (port) | ||||
| spar | volt x105 | PAR (starboard) | ||||
| speed | m s-1 | Relative wind speed | ||||
| direct | degrees | Relative wind direction | ||||
| airtemp | deg C | Air temperature | ||||
| humidity | % | Relative humidity | ||||
| ptir | volt x105 | TIR (port) | ||||
| stir | volt x105 | TIR (starboard) |
All the reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, missing data by both setting the data to an appropriate value and setting the quality control flag.
Calibration
Field Calibrations
Currently, no independent data are available for calibration against samples.
Manufacturer's Calibrations
Chlorophyll-a
The following manufacturer's calibration was applied to the WETStar fluorometer (s/n WS3S - 246) to derive chlorophyll-a concentration:
|
CHL (µg L-1) = SF x (a - CWO) |
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where 'a' is the raw voltage output, the scale factor (SF) = 13.8 µg V-1 and the clean water offset (CWO) = 0.056 V (1 µg L-1 = 1 mg m-3)
Transmittance and beam attenuation
The following manufacturer's calibration was applied to the CStar transmissometer (s/n CST-1132PR) to derive transmittance and beam attenuation:
| light transmission (%) = M x volts + B | ||||||||||||||||||||||||||||||||||||||||
where M = ( Tw / [W0 - Y0] ) (A0 - Y0) / (A1 - Y1) = 21.64502 and B = - M x Y1 = -1.27706.
|
A0 = Vair = factory voltage output in air (manufacturer factory calibration) A1 = Vair = current (most recent) voltage output in air Y0 = Vd = factory dark or zero (blocked path) voltage (manufacturer factory calibration) Y1 = Vd = current (most recent) dark or zero (blocked path) voltage W0 = Vref = factory voltage output in pure water (manufacturer factory calibration) Tw = % transmission in pure water = 100% Vdark =0.059 V Vair = 4.784 V Vref = 4.679 V |
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The following manufacturer's equation was applied to transmittance to derive beam attenuation:
| Attenuance (m-1) = (-1/a) x ln(Tr) | ||||||||||||||||||||||||||||||||||||||||
where a is the pathlength in metres (=0.25 m) and Tr is the decimal transmittance (=light transmission(%)/100).
Project Information
Oceans 2025 - The NERC Marine Centres' Strategic Research Programme 2007-2012
Who funds the programme?
The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).
Who is involved in the programme?
The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:
- National Oceanography Centre, Southampton (NOCS)
- Plymouth Marine Laboratory (PML)
- Marine Biological Association (MBA)
- Sir Alister Hardy Foundation for Marine Science (SAHFOS)
- Proudman Oceanographic Laboratory (POL)
- Scottish Association for Marine Science (SAMS)
- Sea Mammal Research Unit (SMRU)
Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:
- British Oceanographic Data Centre (BODC), hosted at POL
- Permanent Service for Mean Sea Level (PSMSL), hosted at POL
- Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS
The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.
What is the programme about?
Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:
- improve knowledge of how the seas behave, not just now but in the future;
- help assess what that might mean for the Earth system and for society;
- assist in developing sustainable solutions for the management of marine resources for future generations;
- enhance the research capabilities and facilities available for UK marine science.
In order to address these aims there are nine science themes supported by the Oceans 2025 programme:
- Climate, circulation and sea level (Theme 1)
- Marine biogeochemical cycles (Theme 2)
- Shelf and coastal processes (Theme 3)
- Biodiversity and ecosystem functioning (Theme 4)
- Continental margins and deep ocean (Theme 5)
- Sustainable marine resources (Theme 6)
- Technology development (Theme 8)
- Next generation ocean prediction (Theme 9)
- Integration of sustained observations in the marine environment (Theme 10)
In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.
When is the programme active?
The programme started in April 2007 with funding for 5 years.
Brief summary of the programme fieldwork/data
Programme fieldwork and data collection are to be achieved through:
- physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;
- the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';
- physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;
- coastal and shelf sea observatory data (Liverpool Bay Coastal Observatory (LBCO) and Western Channel Observatory (WCO)) using the RV Prince Madog and RV Quest.
The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.
Data Activity or Cruise Information
Cruise
| Cruise Name | JC071 |
| Departure Date | 2012-04-29 |
| Arrival Date | 2012-05-12 |
| Principal Scientist(s) | Richard Stephen Lampitt (National Oceanography Centre, Southampton) |
| 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 |
