Metadata Report for BODC Series Reference Number 1761325
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
OSMOSIS RRS James Cook JC090 Surface Hydrography Quality Report
The non-toxic was briefly off between 09:09:00 and 09:24:00 on 08/09/2013 for maintenance. BODC have flagged all channels associated to this for this time period including chlorophyll, fluorescence and transmittance.
BODC applied M flags to chlorophyll fluorescence and transmittance on 14/09/2013 10:27:00 - 10:29:00 due to a dip in transmittance.
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.
OSMOSIS RRS James Cook JC090 Surface Hydrography Instrumentation
The depth of seawater intake was at 5.5 m.
| Manufacturer | Model | Serial number | Last manufacturer's calibration date | Comments |
| WETLabs | WETStar | WS3S-117 | 12/06/2013 | - |
| WETLabs | CSTAR | CST-1132PR | 19/7/2012 | - |
| Sea-Bird | SBE38 | 3854115-0490 | 12/12/2012 | - |
| Sea-Bird | SBE45 | 4548881-0230 | 27/11/2012 | - |
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.
OSMOSIS RRS James Cook JC090 Surface Hydrography processing procedures
Originator's Data Processing
Data was extracted from TECHSAS SBE45-SBE45_JC1.TSG data stream each day and concatenated into a single file in time order. Time was converted from TECHSAS days to seconds from time origin (1/1/2013 0:0:0).
Conductivity was calibrated to bottle samples collected from the ship underway seawater inlet by calculating a time based correction factor = 2.4543E-9*time - 0.07596 which was added to the measured conductivity.
Files delivered to BODC
| Filename | Content description | Format | Interval | Start date/time (UTC) | E nd date/time (UTC) | Comments |
| SBE45_SBE45_JC1_TSG | SBE 45 and SBE 38 only | Matlab | 1 second | 01/09/2013 08:47 | 14/09/2013 23:59 | SBE 45 and SBE 38 data which is not delayed in time |
| Surf_JC_SM_JC1_SURFMETv2 | All raw surfmet data | Matlab | <1 second | 01/09/2013 12:37 | 14/09/2013 23:59 | All sea surface hydrography data but the SBE45 and SBE 38 may be delayed in time. |
BODC Data Processing
Files SBE45_SBE45_JC1_TSG and Surf_JC_SM_JC1_SURFMETv2 were selected for transfer into BODC format since they contained the most accurate version of sea surface hydrography data. The TSG (salinity, housing temperature and conductivity) and sea surface temperature data were sourced from the SBE45_SBE45_JC1_TSG data stream since the same variables in Surf_JC_SM_JC1_SURFMETv2 may be delayed in time.
The files were 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_SBE45_JC1_TSG
| Originator's variable | Originator's units | Description | BODC Code | BODC Units | Unit conversion | Comments |
| temp_h | degrees C | Temperature of conductivity measurement by thermosalinograph | TMESSG01 | degrees C | ||
| conductivity | S/m | Electrical conductivity of the water body by thermosalinograph | CNDCSG01 | S/m | ||
| salinity | PSU | Practical salinity of the water body by thermosalinograph and computation using UNESCO 1983 algorithm and calibration against independent measurements | PSALSG01 | dimensionless | ||
| temp_r | degrees C | Temperature of the water body by thermosalinograph hull sensor and NO verification against independent measurements | TEMPHU01 | degrees C |
Surf_JC_SM_JC1_SURFMETv2
| Originator's variable | Originator's units | Description | BODC Code | BODC Units | Unit conversion | Comments |
| fluorescence | volts | Instrument output (voltage) by linear-response chlorophyll fluorometer | FVLTWS01 | volts | ||
| transmittance | volts | Instrument output (voltage) by 25cm path length red light transmissometer | TVLTDR01 | volts |
Screening
All the reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag.
Calibration
Chlorophyll
| CHL (µg L-1) = SF x (a - CWO) | ||||||||||||||||||||||||||||||||||||||||
where 'a' is the raw voltage output, the scale factor (SF) = 5.1 µg l-1 V-1 and the clean water offset (CWO) = 0.069 µg V-1 (1 µg L-1 = 1 mg m-3).
Transmittance
The following manufacturer's calibration was applied to the transmissometer to derive transmittance:
| light transmission (%) = M x volts + B | ||||||||||||||||||||||||||||||||||||||||
where M = ( Tw / [W0 - Y0] ) * (A0 - Y0) / (A1 - Y1) = 21.7155266015201 and B = - M x Y1 = -1.302931596.
| 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 =0.060 V Vair = 4.758 V Vref = 4.665 V | ||||||||||||||||||||||||||||||||||||||||
Project Information
Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study (OSMOSIS)
Background
The Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study (OSMOSIS) consortium was funded to deliver NERC's Ocean Surface Boundary Layer (OSBL) programme. Commencing in 2011, this multiple year study will combine traditional observational techniques, such as moorings and CTDs, with the latest autonomous sampling technologies (including ocean gliders), capable of delivering near real-time scientific measurements through the water column.
The OSMOSIS consortium aims to improve understanding of the OSBL, the interface between the atmosphere and the deeper ocean. This layer of the water column is thought to play a pivotal role in global climate and the productivity of our oceans.
OSMOSIS involves collaborations between scientists at various universities (Reading, Oxford, Bangor, Southampton and East Anglia) together with researchers at the National Oceanography Centre (NOC), Scottish Association for Marine Science (SAMS) and Plymouth Marine Laboratory (PML). In addition, there are a number of project partners linked to the consortium.
Scientific Objectives
- The primary goal of the fieldwork component of OSMOSIS is to obtain a year-long time series of the properties of the OSBL and its controlling 3D physical processes. This is achieved with an array of moorings (two nested clusters of 4 moorings, each centred around a central mooring) and gliders deployed near the Porcupine Abyssal Plain (PAP) observatory. Data obtained from this campaign will help with the understanding of these processes and subsequent development of associated parameterisations.
- OSMOSIS will attempt to create parameterisations for the processes which determine the evolving stratification and potential vorticity budgets of the OSBL.
- The overall legacy of OSMOSIS will be to develop new (physically based and observationally supported) parameterisations of processes that deepen and shoal the OSBL, and to implement and evaluate these parameterisations in a state-of-the-art global coupled climate model, facilitating improved weather and climate predictions.
Fieldwork
Three cruises are directly associated with the OSMOSIS consortium. Preliminary exploratory work in the Clyde Sea (September 2011) to hone techniques and strategies, followed by a mooring deployment and recovery cruise in the vicinity of the Porcupine Abyssal Plain (PAP) observatory (in late Summer 2012 and 2013 respectively). Additional opportunist ship time being factored in to support the ambitious glider operations associated with OSMOSIS.
Instrumentation
Types of instrumentation and measurements associated with the OSMOSIS observational campaign:
- Ocean gliders
- Wave rider buoys
- Towed SeaSoar surveys
- Microshear measurements
- Moored current meters, conductivity-temperature sensors and ADCPs
- Traditional shipboard measurements (including CTD, underway, discrete nutrients, LADCP, ADCP).
Contacts
| Collaborator | Organisation |
|---|---|
| Prof. Stephen Belcher | University of Reading, U.K |
| Dr. Alberto C Naveira Garabato | University of Southampton, U.K |
Data Activity or Cruise Information
Cruise
| Cruise Name | JC090 |
| Departure Date | 2013-08-31 |
| Arrival Date | 2013-09-16 |
| Principal Scientist(s) | Alberto C Naveira Garabato (University of Southampton School of Ocean and Earth Science) |
| 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 |
