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Metadata Report for BODC Series Reference Number 2138565

Metadata Summary

Data Description

Data Category Water sample data
Instrument Type
Niskin bottle  discrete water samplers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Mr Stephen Woodward
Originating Organization University of East Anglia School of Environmental Sciences
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) OSMOSIS

Data Identifiers

Originator's Identifier JC090_CTD_DOXY_842:JC090_001
BODC Series Reference 2138565

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2013-09-03 16:09
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval -

Spatial Co-ordinates

Latitude 48.68029 N ( 48° 40.8' N )
Longitude 16.19081 W ( 16° 11.4' W )
Positional Uncertainty 0.05 to 0.1 n.miles
Minimum Sensor or Sampling Depth 5.3 m
Maximum Sensor or Sampling Depth 998.8 m
Minimum Sensor or Sampling Height 3816.6 m
Maximum Sensor or Sampling Height 4810.1 m
Sea Floor Depth 4815.4 m
Sea Floor Depth Source BUDS
Sensor or Sampling Distribution Unspecified -
Sensor or Sampling Depth Datum Unspecified -
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface


BODC CODERankUnitsTitle
ADEPZZ011MetresDepth (spatial coordinate) relative to water surface in the water body
BOTTFLAG1Not applicableSampling process quality flag (BODC C22)
DOKGWITX1Micromoles per kilogramConcentration of oxygen {O2 CAS 7782-44-7} per unit mass of the water body [dissolved plus reactive particulate phase] by Winkler titration
FIRSEQID1DimensionlessBottle firing sequence number
ROSPOSID1DimensionlessBottle rosette position identifier
SAMPRFNM1DimensionlessSample reference number

Definition of BOTTFLAG

0The sampling event occurred without any incident being reported to BODC.
1The filter in an in-situ sampling pump physically ruptured during sample resulting in an unquantifiable loss of sampled material.
2Analytical evidence (e.g. surface water salinity measured on a sample collected at depth) indicates that the water sample has been contaminated by water from depths other than the depths of sampling.
3The feedback indicator on the deck unit reported that the bottle closure command had failed. General Oceanics deck units used on NERC vessels in the 80s and 90s were renowned for reporting misfires when the bottle had been closed. This flag is also suitable for when a trigger command is mistakenly sent to a bottle that has previously been fired.
4During the sampling deployment the bottle was fired in an order other than incrementing rosette position. Indicative of the potential for errors in the assignment of bottle firing depth, especially with General Oceanics rosettes.
5Water was reported to be escaping from the bottle as the rosette was being recovered.
6The bottle seals were observed to be incorrectly seated and the bottle was only part full of water on recovery.
7Either the bottle was found to contain no sample on recovery or there was no bottle fitted to the rosette position fired (but SBE35 record may exist).
8There is reason to doubt the accuracy of the sampling depth associated with the sample.
9The bottle air vent had not been closed prior to deployment giving rise to a risk of sample contamination through leakage.

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

Problem Reports

No Problem Report Found in the Database

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

Niskin Bottle

The Niskin bottle is a device used by oceanographers to collect subsurface seawater samples. It is a plastic bottle with caps and rubber seals at each end and is deployed with the caps held open, allowing free-flushing of the bottle as it moves through the water column.

Standard Niskin

The standard version of the bottle includes a plastic-coated metal spring or elastic cord running through the interior of the bottle that joins the two caps, and the caps are held open against the spring by plastic lanyards. When the bottle reaches the desired depth the lanyards are released by a pressure-actuated switch, command signal or messenger weight and the caps are forced shut and sealed, trapping the seawater sample.

Lever Action Niskin

The Lever Action Niskin Bottle differs from the standard version, in that the caps are held open during deployment by externally mounted stainless steel springs rather than an internal spring or cord. Lever Action Niskins are recommended for applications where a completely clear sample chamber is critical or for use in deep cold water.

Clean Sampling

A modified version of the standard Niskin bottle has been developed for clean sampling. This is teflon-coated and uses a latex cord to close the caps rather than a metal spring. The clean version of the Levered Action Niskin bottle is also teflon-coated and uses epoxy covered springs in place of the stainless steel springs. These bottles are specifically designed to minimise metal contamination when sampling trace metals.


Bottles may be deployed singly clamped to a wire or in groups of up to 48 on a rosette. Standard bottles and Lever Action bottles have a capacity between 1.7 and 30 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.

JC090 Discrete CTD Oxygen Sampling Document

The following contains extracts from the JC090 cruise report.

Originator's Protocol for Data Acquisition and Analysis

The RRS James Cook 090 cruise was the concluding phase of the fieldwork for the Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study (OSMOSIS) consortium and sought to recover 9 moorings and 2 gliders, to conduct hydrographic and biogeochemical measurements for mooring and glider calibration, and to obtain opportunistic measurements of upper-ocean microstructure and air-sea CO2 fluxes. The cruise departed on the 31 August 2013 from the port of Vigo, Spain and returned on the 16 September 2013 at the port of Santander, Spain.

Sample collection

Water samples were collected for determination of dissolved oxygen concentrations. Samples were taken from two 1000 m CTD casts which calibrated the Aanderaa oxygen optode sensors on seagliders SG533 and SG566 and from a 200 m CTD cast which calibrated the WetLabs sensor, close to the gliders' positions at the South West outer mooring. Samples also provided a calibration of the CTD oxygen sensor.

Calibrated volumes of 125 ml borosilicate glass Iodine flasks were rinsed with water drawn from the same Niskin bottle for 30-40 seconds. The flask was then filled completely, checking for the absence of air bubbles. The temperature of the water samples were recorded at the time of sampling using a handheld digital temperature probe. To fix the oxygen, 1 cm3 of 3 mol dm-3 Manganese Chloride Tetrahydrate (MnCl2) and 1.00 cm3 4.0 mol dm-3 Sodium Iodide/8.0 mol dm-3 Sodium Hydroxide (NaOH/NaI) were added. Samples were then sealed and shaken to mix the reagents. The shaking was repeated after 20-30 minutes and then left overnight.

Sample analysis

Sampling analysis was performed in a temperature controlled lab (20° C) on the RRS James Cook. Each sample had 1 cm3 of 5 mol dm-3 Sulphuric acid added to the sample along with a magnetic stir bar. Titration was performed with 0.2 mol dm-3 Sodium Thiosulphate Pentahydrate till end point. Prior to the analysis of each batch of samples, two test samples containing fixed tap water were titrated, and a further test sample was titrated after each pause in the sequence of analysis. The temperature was recorded at the time of titration using a handheld digital temperature probe.

BODC Data Processing Procedures

Discrete oxygen samples were provided to BODC in Mstar format. The Mstar software is written in Matlab and stores the data in NetCDF. Oxygen values, together with associated rosette positions and WOCE bottle flags, were extracted from the Mstar files and saved in .csv format.

Bottle firing pressures were extracted from Sea-Bird .btl files (also provided by the Data Originator) and merged with the sample data. Depths were derived from the pressures by BODC.

The data were loaded to BODC's ORACLE Relational Database. Data that were considered unrealistic were flagged suspect.

Content of data series

Originator's Parameter Unit Description BODC Parameter code BODC Unit Comments
Oxygen µmol/kg Concentration of oxygen {O2} per unit mass of the water body [dissolved plus reactive particulate phase] by Winkler titration DOKGWITX µmol/kg No unit conversion necessary


Naveira-Garabato, A. C. et al. (2013). 'Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study (OSMOSIS)'. Cruise Report No. 25 National Oceanography Centre, Southampton.

Project Information

Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study (OSMOSIS)


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.


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.


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).


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

Data Activity

Start Date (yyyy-mm-dd) 2013-09-03
End Date (yyyy-mm-dd) 2013-09-03
Organization Undertaking ActivityUniversity of Southampton School of Ocean and Earth Science
Country of OrganizationUnited Kingdom
Originator's Data Activity IdentifierJC090_CTD_JC090_001
Platform Categorylowered unmanned submersible

BODC Sample Metadata Report for JC090_CTD_JC090_001

Sample reference number Nominal collection volume(l) Bottle rosette position Bottle firing sequence number Minimum pressure sampled (dbar) Maximum pressure sampled (dbar) Depth of sampling point (m) Bottle type Sample quality flag Bottle reference Comments
886766   20.00 1 1 1009.30 1010.30  998.80 Niskin bottle No problem reported    
886769   20.00 3 3  809.30  810.30  801.40 Niskin bottle No problem reported    
886772   20.00 4 4  707.40  708.40  700.70 Niskin bottle No problem reported    
886775   20.00 5 5  707.00  708.00  700.30 Niskin bottle No problem reported    
886778   20.00 6 6  607.10  608.10  601.60 Niskin bottle No problem reported    
886781   20.00 7 7  504.30  505.30  499.90 Niskin bottle No problem reported    
886784   20.00 9 9  404.20  405.20  400.90 Niskin bottle No problem reported    
886787   20.00 10 10  303.70  304.70  301.40 Niskin bottle No problem reported    
886790   20.00 12 12  201.90  202.90  200.60 Niskin bottle No problem reported    
886793   20.00 13 13  102.40  103.40  102.00 Niskin bottle No problem reported    
886796   20.00 14 14  102.00  103.00  101.60 Niskin bottle No problem reported    
886799   20.00 17 17   47.70   48.70   47.80 Niskin bottle No problem reported    
886802   20.00 19 19   34.70   35.70   34.90 Niskin bottle No problem reported    
886805   20.00 21 21   19.50   20.50   19.80 Niskin bottle No problem reported    
886808   20.00 23 23    4.80    5.80    5.30 Niskin bottle No problem reported    
906860   20.00 2 2 1008.20 1009.20  997.70 Niskin bottle No problem reported    
906863   20.00 8 8  505.40  506.40  501.00 Niskin bottle No problem reported    
906866   20.00 11 11  304.10  305.10  301.80 Niskin bottle No problem reported    
906869   20.00 15 15   75.60   76.60   75.40 Niskin bottle No problem reported    
906872   20.00 16 16   61.00   62.00   61.00 Niskin bottle Bottle leak    
906875   20.00 18 18   47.60   48.60   47.70 Niskin bottle No problem reported    
906878   20.00 20 20   34.70   35.70   34.90 Niskin bottle No problem reported    
906881   20.00 22 22   19.70   20.70   20.00 Niskin bottle No problem reported    
906884   20.00 24 24    4.80    5.80    5.30 Niskin bottle No problem reported    

Please note:the supplied parameters may not have been sampled from all the bottle firings described in the table above. Cross-match the Sample Reference Number above against the SAMPRFNM value in the data file to identify the relevant metadata.

Related Data Activity activities are detailed in Appendix 1


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

Appendix 1: JC090_CTD_JC090_001

Related series for this Data Activity are presented in the table below. Further information can be found by following the appropriate links.

If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.

Series IdentifierData CategoryStart date/timeStart positionCruise
2138473Water sample data2013-09-03 16:09:3848.68029 N, 16.19081 WRRS James Cook JC090
2138608Water sample data2013-09-03 16:09:3848.68029 N, 16.19081 WRRS James Cook JC090