OceanSITES User`s Manual
Contents
1. Data mode Indicates if the data point is real time delayed or post recovery mode It is included when the dataset mixes modes for a single variable See note on data modes below and reference table 5 long_name type char Required fixed value conventions type char Required fixed value flag_values type char Required fixed value flag_meanings type char Required fixed value FillValue type char Required fixed value Overall uncertainty of the data given in lt PARAM gt Cf note on uncertainty below long_name type char Required fixed value _ FillValue type float Required units type char Required Must be the same as lt PARAM gt units The quality of the data in a variable lt PARAM gt is described by the attribute lt PARAM gt QC_procedure and one of the following the attribute lt PARAM gt QC_indicator or the variable lt PARAM_QC gt PARAM QC procedure is mandatory and contains values from reference table 2 1 which describe what kind of quality control procedure has been applied It is mandatory to define one of PARAM QC indicator or lt PARAM_QC gt both of which would contain values describing the data quality as per reference table 2 If the quality is the same for all lt PARAMS use PARAM QC indicator Else use PARAM QC Note on uncertainty If the overall measurement uncertainty for a variable lt PARAM gt is reasonably well known it must be provided in the a2. Scripps USA WHOI Woods Hole Oceanographic Institution USA 5 5 Reference table 5 data mode The values for the variables lt PARAM gt _DM the global attribute data mode and variable attributes lt PARAM gt DM_ indicator are defined as follows Value Meaning Real time data Data coming from the typically remote platform through a communication channel without physical access to the instruments disassembly or recovery of the platform Example for a mooring with a radio communication this would be data obtained through the radio Post recovery data Data obtained after the instruments or the platform have been recovered or p serviced Example for instruments on a mooring this would be data downloaded directly from the instruments after the mooring has been recovered on a ship Delayed mode data Data published after all calibrations and quality control procedures have been applied This is the final status of the data Mixed This value is only allowed in the global attribute data mode or in attributes to variables in the form PARAM DM indicator It indicates that the file contains data in more than one of the above states In this case the variable s PARAM DM specify which data is in which data mode 5 6 Reference table 6 OceanSITES sites catalog The OceanSITES sites catalog is available at http www oceansites org parameters The following list is an extract from the catalog Oce
3. e YYY configuration code e ZZZ list of data codes from reference table 1 The data code is a list of the primary parameters measured The data code will not list secondary parameters d e lt _PARTX gt when an OceanSites data file size becomes excessive eg gt 100MD it can be split in smaller parts PARTI PART2 PARTN Example OS CIS 1 200502 TS nc This file contains temperature and salinity data from the CIS 1 mooring from the Animate project for the deployment performed in February 2005 Giving the deployment date here 200502 as the configuration code YYY is the recommended method if multiple site occupations exist and if this makes identification unique 6 1 2 Metadata file naming convention OS XXX YYY META xml e OS OceanSITES prefix e XXX platform code e YYY configuration code These metadata are for the corresponding data file s OS XXX YYY ZZZ PARTX nc Example e OS CIS 1 200502 META xml This file contains the metadata of CIS 1 mooring for the deployment performed in February 2005 6 2 Index file for data files To allow for data discovery without downloading the data files themselves an index file is created at the GDAC level which lists all available data files and the location and time ranges of their data contents e The data index file is located at the root directory of the GDAC e The index file contains the list and a description of all data files available on
4. of sea water 5 2 Reference table 2 quality control flag scale The quality control flags indicate the data quality of the data values in a file and are normally assigned after quality control procedures have been performed These codes are used in the lt PARAM gt _QC variables to describe the quality of each measurement or in the attribute lt PARAM gt QC_indicator to describe the overall quality of the parameter Code Meaning Real time comment Post recovery mode comment All real time QC tests passed All post recovery tests passed Bad data that are potentially These data are not to be used Possible re calibration needed correctable without scientific correction Bad data Data have failed one or more Data have failed one or more tests tests Value changed Data may be recovered after transmission error DUE poqwu B Nominal value Data were not observed but reported i e an anchor drop position or an instrument target depth as opposed to a GPS position time series or a pressure sensor time series Interpolated value Missing data may be interpolated from neighbouring data in space or time 5 2 1 Reference table 2 1 quality control procedure indicator This table describes the quality procedures applied to all the measurement of a parameter These values are used as an overall quality indicator i e one summarizing all measurements in the attributes of each variable lt PARAM gt Cf PARAM QC proc
5. Investigator long_name type char standard name type char see reference table 3 units type char see reference table 3 FillValue type float see reference table 3 QC indicator type byte see reference table 2 and note on quality control below QC procedure type byte see reference table 2 1 and note on quality control below valid min type float Minimum value for valid data valid max type float Maximum value for valid data comment type char Any free format text with comments as appropriate sensor depth type float Nominal sensor depth s in meters counting positive as per DEPTH positive ancillary variables type char Other variables associated with lt PARAM e g lt PARAM gt _QC List as space separated string Example TEMP ancillary variablesz TEMP QC TEMP DM TEMP UNCERTAINTY uncertainty type float Overall measurement uncertainty if constant Cf note on uncertainty below accuracy type float Nominal sensor accuracy Cf note on uncertainty below precision type float Nominal sensor precision Cf note on uncertainty below resolution type float Nominal resolution of this data parameter cell methods type char Specifies cell method as per CF convention Example TEMP cell_methods TIME point DEPTH point LATITUDE point LONGITUDE point Values are listed in table 2 2 DM indicator Type char Data mode if constant as per reference table 5 Cf note on data modes below Byte lt PARAM
6. QC procedure Y LONGITUDE uncertainty lt Z gt LONGITUDE comment Optional comment LONGITUDE axis X Float DEPTH DEPTH DEPTH long_name Depth of each measurement DEPTH standard_name depth DEPTH units meters DEPTH positive down DEPTH FillValue 99999 0 DEPTH valid min 0 0 DEPTH valid max 12000 0 DEPTH QC indicator X DEPTH QC procedure Y DEPTH uncertainty Z DEPTH comment Optional comment DEPTH axis Z Comment Date and time UTC of the measurement in days since midnight 1950 01 01 Example Noon Jan 2 1950 is stored as 1 5 July 25 2001 19 14 00 is stored as 18833 8013889885 X Replaces TIME QC if constant Cf note on quality control in data variable section value from reference table 2 Y Cf note on quality control in data variable section value from reference table 2 1 Z Choose appropriate value Latitude of the measurements Units degrees north southern latitudes are negative Example 44 4991 for 44 29 56 76 N X Replaces LATITUDE QC if constant Cf note on quality control in data variable section value from reference table 2 Y Cf note on quality control in data variable section value from reference table 2 1 lt Z gt Choose appropriate value Longitude of the measurements Unit degrees east western latitudes are negative Example 16 7222for 16 43 19 92 E X Replaces LONGI
7. e The NetCDF standard name attribute contains the standardized parameter name from CF conventions e The NetCDF units attribute are compliant with Udunits as implemented in the CF COARDS standards As the parameter names are not strictly standardized one should use the standard name attribute to query a particular measurement from differe nt data files Example On a mooring sea temperature measured by a series of Microcat CTD is reported as TEMP with a standard name of SEA WATER TEMPERATURE Secondary temperature measurement performed by an oxygen sensor is reported as DOXY TEMP with a standard name of temperature of sensor for oxygen in sea water For both measurements the unit attribute is degree Celsius References The OceanSITES standard names are taken from the CF standard names available at e http c pcmdi lInl gov documents cf standard names The parameter names are based on SeaDataNet BODC parameter discovery vocabulary available at e http seadatanet maris2 nl v_bodc_vocab welcome aspx Select P021 BODC Parameter Discovery Vocabulary The units are compliant with Udunits as implemented by the CF standard definitions are available at e http www unidata ucar edu software udunits The valid parameter names standard names long names and units are available at e http www ifremer fr co etc oceansites oceansites user manual parameters pdf e http www ifremer fr co etc oceansites oceansites
8. gt _QC TIME DEPTH lt PARAM gt _QC long_name quality flag lt PARAM gt _QC conventions OceanSITES reference table 2 lt PARAM gt _QC _ FillValue 128 PARAM QO valid min 0 lt PARAM gt _QC valid_max 9 PARAM QC flag values 0 1 2 3 4 5 7 8 9 lt PARAM gt _QC flag_meanings no_qc_performed good_data probably good data bad data that are potentially correcta ble bad data value changed not used nominal value interpolated value missing value Char PARAM DM TIME DEPTH PARAM DM long name method of data processing PARAM DM conventions OceanSITES reference table 5 PARAM DMf lag values R P D M PARAM DM jlag meanings real time postrecovery delayed mode mixed PARAM DM FillValue Float PARAM UNCERTAINTY TIME DEPTH PARAM UNCERTAINTY long name uncertainty PARAM UNCERTAINTY FillValue Y lt PARAM gt units lt Y gt Note on quality control QC Contains quality flags for values of associated lt PARAMS gt Flag scale is specified in reference table 2 and is included in the flag_meanings attribute long_name type char fixed value conventions type char Required fixed value _FillValue type byte Required fixed value valid_min type byte Required fixed value valid_max type byte Required fixed value flag_values type byte Required fixed value flag_meanings type char Required fixed value
9. user manual units pdf The following list an extract of the OceanSITES parameter dictionary for parameter name and standard name Parameter Standard name AIRT air_temperature ATMP air_pressure ATMS CDIR CNDC CSPD DEPH air_pressure_at_sea_level direction_of_sea_water_velocity was sea_water_direction sea_water_electrical_conductivity sea_water_speed depth DEWT dew_point_temperature DOX2 DOXY DOXY_TEM moles_of_oxygen_per_unit_mass_in_sea_water was dissolved_oxygen mass_concentration_of_oxygen_in_sea_water was dissolved_oxygen temperature_of_sensor_for_oxygen_in_sea_water DRYT dry_bulb_temperature DYNHT EWCT FLU2 HCSP HEAT dynamic_height eastward_sea_water_velocity fluorescence sea_water_speed heat_content ISO17 isotherm depth z surface downwelling longwave flux in air northward sea water velocity optical backscattering coefficient surface partial pressure of carbon dioxide in air was CO2 partial pressure in dry wet gas sea water pressure sea water salinity rainfall rate thickness of rainfall amount relative humidity surface downwelling shortwave flux in air isotropic shortwave radiance in air z surface downwelling shortwave flux in air TEMP sea_water_temperature wind_to_direction WSPD wind_speed WSPD wind_speed 5 4 Reference table 4 Data Assembly Center Codes Data Assembly Centers and institutions NDBC National Data Buoy Center USA SIO
10. DAC where they are made publicly available The user can access the data at either GDAC cf section GDAC organization 2 OceanSITES data format OceanSITES uses the NetCDF network Common Data Form system a set of software libraries and machine independent data formats Our implementation of NetCDF is based on the community supported Climate and Forecast CF specification which supplies a standard vocabulary and some metadata conventions OceanSITES has several more restrictions than the CF standard These are intended to make it easier to share in situ data to make it simpler for the GDACs to aggregate data from multiple sites and to ensure that the data can be created and understood by the basic NetCDF utilities e OceanSITES includes standard terms for the short name of both coordinate and data variables measurements e File names are created using a standard described in section 6 2 Coordinate variables which describe the dimensions of a data set are limited to a single set of longitude latitude depth and time X Y Z and T dimensions in any single file If data from a reference station cannot all be put on to a single set of axes then separate files are created for these data An OceanSITES data file contains measurements such as temperature and salinity continuously performed at different levels on a platform e g mooring as well as meteorological or other parameters recorded at the site derived variables assoc
11. EP error 0 02f TEMP cell_methods TIME point DEPTH point LATITUDE point LONGITUDE point TEMP DM indicator z P Byte TEMP QC TIME LEVEL TEMP QcC long name quality flag TEMP QC conventions OceanSITES reference table 2 TEMP QcC flag values 0 1 2 3 4 5 7 8 9 TEMP QcC flag meanings no qc performed good data probably good data bad data that are potentially correctable bad data value changed not used nominal value interpolated value missing value TEMP QC HilValue 0 4 OceanSITES metadata format The OceanSITES data management team is developing a metadata format probably using a SensorML implementation of XML to allow metadata to be stored external to the NetCDF files 5 Reference tables 5 1 Reference tables 1 data type and data code 5 1 1 Data type The data type global attribute should have one of the following valid values Data type OceanSITES metadata OceanSITES profile data OceanSITES time series data OceanSITES trajectory data 5 1 2 Data code Data codes are used for file naming convention in chapter 6 1 1 and describe what kind of measurements the file contains They consist of the following letters Data Code Meaning Conductivity electric conductivity of sea water Mo Meteorological parameters e g wind air pressure radiative fluxes air temperature lO Oxygen concentration in sea water Salinity of sea water Temperature of sea water Velocity
12. TUDE QC if constant Cf note on quality control in data variable section value from reference table 2 Y Cf note on quality control in data variable section value from reference table 2 1 Z Choose appropriate value Depth of each measurement Example 513 for a measurement 513 meters below sea surface Z axes may be positive up atmospheric or positive down Oceanic X Replaces DEPTH QC if constant Cf note on quality control in data variable section value from reference table 2 Y Cf note on quality control in data variable section value from reference table 2 1 lt Z gt Choose appropriate value 3 2 2 Coordinate quality control variables The coordinate variables have the same quality control variables as the data variables If the quality control values are constant the information is given in attributes of the coordinate variables For details see lt PARAM gt _QC in the section on data variables and the note on quality control therein Type Name Dimension Attributes Comment Byte TIME_QC TIME Quality flag for each TIME value Byte POSITION_QC POSITION Quality flag for each LATITUDE and LONGITUDE value Byte DEPTH QC DEPTH Quality flag for each DEPTH value 3 2 3 Data variables Data variables contain the actual measurements and indicators about their quality uncertainty and mode through which they were obtained There are different options as to how the indicators are
13. a OceanSITES Taking the pulse of the global ocean OceanSITES User s Manual NetCDF Conventions and Reference Tables Version 1 1 June 30 2008 Table of contents 1 0VERVIEW 1 1 About OceanSITES 1 2 About this document 1 3 OceanSITES data management structure and data access 2 OCEANSITES DATA FORMAT 3 DATA FILE DIMENSIONS 3 1 Global attributes 3 2 Variables 3 2 1 Coordinate variables 3 2 2 Coordinate quality control variables 3 2 3 Data variables 4 OCEANSITES METADATA FORMAT 5 REFERENCE TABLES 5 1 Reference tables 1 data type and data code 5 1 1 Data type 5 1 2 Data code 5 2 Reference table 2 quality control flag scale 5 2 1 Reference table 2 1 quality control procedure indicator 5 2 2 Reference table 2 2 cell methods 5 3 Reference table 3 OceanSITES parameter dictionary 5 4 Reference table 4 Data Assembly Center Codes 5 5 Reference table 5 data mode 5 6 Reference table 6 OceanSITES sites catalog 6 GDAC ORGANIZATION 6 1 File naming convention 6 1 1 Data file naming convention 6 1 2 Metadata file naming convention 6 2 Index file for data files 11 11 13 14 17 17 17 17 17 18 18 19 19 22 22 23 24 24 24 25 25 History Version DELG Comment 0 1 20 03 2003 TC creation of the document 0 3 20 02 2004 TC updates on locations mooring name data state indicator parameters table epic codes history information 26 05 2004 N G make more flexible add d
14. amples for a mooring without positioning system LATITUDE 1 For a mooring with a GPS receiver use LATITUDE of the same dimension as TIME and provide the actual location LONGITUDE LONGITUDE 1 Dimension of the LONGITUDE coordinate variable Examples for a mooring without positioning system LONGITUDE 1 For a mooring with a GPS receiver use LONGITUDE of the same dimension as TIME and provide the actual location POSITION POSITION 1 Dimension of the POSITION_QC variable 3 1 Global attributes The global attribute section of a NetCDF file contains metadata that descibes the contents of the file overall and allows for data discovery All fields should be human readable and should be of character type not numeric even if the information content is a number OceanSITES recommends that all of these attributes be used and contain meaningful information unless there are technical reasons rendering this impossible However files that do not at least contain the attributes listed as mandatory will not be considered OceanSITES compliant In OceanSITES global attribute names are in lower case letters Global attributes can be thought of as conveying five kinds of information e What what are the data in this dataset e Where the spatial coverage of the data e When the temporal coverage of the data e Who who produced the data e How how were the data produced and made available The global attributes specification follows the recomm
15. anSITES moorings catalogue based on data files available from GDAC WMO site code platform code code contact mw me pes em Ds e OE MOVE V6 41174 INDBC SS NTAS NTAS NDBC Hole Woods STRATUS STRATUS NDBC Hole oer 6 GDAC organization There are two GDACs global data assembly centers for redundancy which are the users access points for OceanSITES data One GDAC is located in France Coriolis http www coriolis eu org the other one in the USA NDBC National Data Buoy Center http www ndbc noaa gov The GDACs handle OceanSITES data metadata and index files on ftp servers The servers at both GDACS are synchronized at least daily to provide the same OceanSITES data The user can access the data at either GDAC s ftp site e ftp ftp ifremer fr ifremer oceansites e ftp data ndbc noaa gov data oceansites From these root directories of the GDACs downward the organization of the directories and files is e site plattorm OS XXX YYY ZZZ PARTX nc Site OceanSites site code e platform platform code The site and platform codes are available in the O ceanSITES catalogue document at either GDAC s root directory e oceansites catalogue xml 6 1 File naming convention The OceanSITES file names use the following naming conventions 6 1 1 Data file naming convention OS XXX YYY ZAZZ PARIX nc e OS OceanSITES prefix e XXX platform code from the OceanSITES catalogue
16. ataset metadata file 0 4 01 06 2004 TC separate data set description and data file merge with Steve Hankins s straw man 28 06 2004 TC updates from Nan Galbraith Steve Hankins Jonathan Gregory Brian Eaton 23 05 2005 Maureen Edwards NOCS data centre new GF3 parameters 0 7 24 05 2005 Roy Lowry physical parameters from BODC Data Markup Vocabulary 1 0 18 02 2006 TC updates following OceanSITES data management meeting 2006 Hawai i 82 1 LEVEL dimension replaces DEPTH to accomadate depth or pressure 82 2 QC MANUAL field created 2 2 CONVENTION field removed 82 2 PLATFORM CODE added 2 2 SITE CODE added 2 2 WMO PLATFORM CODE added 82 3 DEPTH renamed DEPH to comply to GF3 82 3 DATA MODE set at measurement level 83 metadata file description transferred to OceanSITES metadata proposal until approval 5 file naming convention updated 19 02 2006 NG data codes in chapter 4 1 2 28 04 2006 PF amp NG data mode optional 28 04 2006 TC amp JG 82 2 global attributes 1 1 April May NG MM TC ML general revision based on OceanSITES 2008 June 2008 meeting Epic codes removed Use ISO8601 for string dates Remove general attributes Update global attribute section for CF 1 1 compatibility New dimensions for DEPTH LATITUDE LONGITUDE Add an uncertainty attribute New presentation of the document 1 Overview 1 1 About OceanSITES The OceanSITES program is the global network of open ocean sustained timeser
17. edure attribute description in section 3 2 3 Code Meaning fo No QC performed Ranges applied bad data flagged Data interpolated B Dna veres sonst noseloraiercrtetial mem 7 Other QC process applied 5 2 2 Reference table 2 2 cell methods From NetCDF Climate and Forecast CF Metadata Conventions Version 1 2 4 May 2008 In the Units column u indicates the units of the physical quantity before the method is applied Cell Method Units Description The data values are representative of points in space or time instantaneous point u The data values are sum u representative of a sum or accumulation over the cell maximum u Maximum median u Median Average of maximum and mid range u minimum minimum u Minimum mean u Mean average value Mode most common mode u value standard_deviation u Standard deviation variance u2 Variance 5 3 Reference table 3 OceanSITES parameter dictionary Convention for parameter names standard names and units The parameter dictionary is now contained in an Excel file which is available at http www oceansites org parameters In the near future it should be available in XML format e Parameter names should start with a 4 characters code based on SeaDataNet BODC parameter discovery vocabulary They are not strictly standardized however When necessary a parameter name has a suffix that designates secondary parameters The suffix starts with the character
18. embly Center DAC in charge of this data file center ROSITES The data_assembly_center are listed in reference table 4 pi_name pi_name Alice Juarez Name of the principal investigator in charge of the platform distribution_state distribution_statement Foll Statement describing data distribution policy OceanSITES has ows CLIVAR Climate adopted the CLIVAR data policy which explicitly calls for free Varibility and Predictability and unrestricted data exchange Details at standards cf http www clivar org data data_policy php http www clivar org data da ta_policy php Data available free of charge User assumes all risk for use of data User must display citation in any publication or product using data User must contact PI prior to any commercial use of data citation citation These data were The citation to be used in publications using the dataset collected and made freely available by the OceanSITES project and the national programs that contribute to it update interval update interval daily Update interval for the file one of the following hourly daily yearly void Use void for delayed mode or archive data that do not need continuous updating qc manual qc manual OceanSITES This field contains the name of the manual that describes the User s Manual v1 1 quality control procedure As of now there is no separate QC manual so the user s manual is the appropriate reference Note on t
19. endations of Unidata NetCDF Attribute Convention for Dataset Discovery at http www unidata ucar edu software netcdf java formats DataDiscovery AttConvention html AEWG Example Definition data_type data_type OceanSITES This field contains the type of data contained in the file time series data The list of acceptable data types is in reference table 1 Example OceanSITES time series data This attribute is mandatory format_version format_version 1 1 OceanSITES format version Example 1 1 This attribute is mandatory platform_code platform_code CIS 1 Platform unique code within OceanSITES project Example CIS 1 mooring on CIS site Central Irminger Sea This attribute is mandatory date_update date_update 2006 0 4 File update or creation date UTC See note on time format 11T08 35 00Z below This attribute is mandatory institution institution National Specifies institution where the original data was produced Oceanographic Centre site_code site code CIS Name of the site within OceanSITES project Example CIS for Central Irminger Sea The site codes are listed in reference table 6 wmo platform c wmo platform code z 48409 WMO World Meteorological Organization identifier j This platform number is unique within the OceanSITES project Example 48409 for CIS 1 mooring source Mooring The method of production of the original data For OceanSITES observation data use one of the following Shi
20. f there is a separate QC variable for that parameter Optionally the Z axis may be represented as pressure if for example pressure is recorded directly by an instrument and the calculation of depth from pressure would cause a loss of information Depth is strongly preferred since it allows data to be used more directly data with different coordinate variables must be recorded in separate files Type Name Dimension Attributes Double TIME TIME TIME long_name time TIME standard_name time TIME units days since 1950 01 01T00 00 00Z TIME FillValue 999999 0 TIME valid min 0 0 TIME valid max 90000 0 TIME QC indicator X TIME QC procedure Y TIME uncertainty Z TIME comment Optional comment TIME axis T Float LATITUDE LATITUDE LATITUDE long_name Latitude of each location LATITUDE standard_name latitude LATITUDE units degrees_north LATITUDE FillValue 99999 0 LATITUDE valid_min 90 0 LATITUDE valid_max 90 0 LATITUDE QC indicator X LATITUDE QC procedure Y LATITUDE uncertainty lt Z gt LATITUDE comment Optional comment LATITUDE axis Y Float LONGITUDE LONGITUDE LONGITUDE long_name Longitude of each location LONGITUDE standard_name longitude LONGITUDE units degrees east LONGITUDE FillValue 99999 0 LONGITUDE valid_min 180 0 LONGITUDE valid_max 180 0 LONGITUDE QC indicator X LONGITUDE
21. iated with the site and complete location time and provenance information The requirements are drawn almost exclusively from the NetCDF Style Guide Units are compliant with CF COARDS Udunits e The time parameter is encoded as recommended by COARDS and CF e Parameters are given standard names from the CF table e Where time is specified as an attribute the ISO8601 standard is used For more information on CF COARDS NetCDF Udunits and ISO8601 see e NetCDF http www unidata ucar edu software netcdf docs BestPractices html e Udunits http www unidata ucar edu software udunits e CF http cEpcemdi lnl gov e COARDS http www ferret noaa gov noaa_coop coop_cdf_profile html e ISO8601 http en wikipedia org wiki ISO_8601 3 Data file dimensions NetCDF dimensions provide information on the size of the data variables OceanSITES allows a single parameter for each of the data dimensions i e time depth latitude and longitude Requirements are described further in the section on coordinate variables Standard names for OceanSITES dimensions should be in upper case Name Comment TIME TIME unlimited Number of time steps Example for a mooring with one value per day and a mission length of one year TIME contains 365 time steps DEPTH DEPTH 5 Number of depth levels Example for a mooring with measurements at 0 25 10 50 100 and 200 meters DEPTH 5 LATITUDE LATITUDE 1 Dimension of the LATITUDE coordinate variable Ex
22. ies sites called ocean reference stations being implemented by an international partnership of researchers OceanSITES provides fixed point timeseries of various physical biogeochemical and atmospheric variables at different locations around the globe from the atmosphere and sea surface to the seafloor The program s objective is to build and maintain a multidisciplinary global network for a broad range of research and operational applications including climate carbon and ecosystem variability and forecasting and ocean state validation All OceanSITES data are publicly available More information about the project is available at http www oceansites org 1 2 About this document The main purpose of this document is to specify the format of the files that are used to distribute OceanSITES data and to document the standards used therein This includes naming conventions or taxomony as well as metadata content 1 3 0ceanSITES data management structure and data access The data flow within OceanSITES is carried out through three organisational units The Principal Investigator PI typically a scientist at a research institution maintains the observing platform and the sensors that deliver the data He or she is responsible for providing the data and all auxiliary information to a Data Assembly Center DAC The DAC assembles OceanSITES compliant files from this information and delivers these to one of two Global Data Assembly Centers G
23. ime formats Whenever time information is given in the global attributes it ought to be a string of the format YYYY MM D DThh mm ssZ i e year month day T hour minute second Z If higher resolution than seconds is needed any number of decimal digits s for the seconds is acceptable YYYY MM D DThh mm ss sZ In any case the time must be in UTC A capital T separates the date and the hour information The string must end with a capital Z an old indication of UTC These formats are two of many described by ISO8601 Examples e 2005 10 24T08 00 00Z e 2008 01 01T22 50 02 031Z 3 2 Variables NetCDF variables include data measured by instruments parameters derived from the primary measurements and coordinate variables which may be nominal values such as values for depth for instruments that do not directly record depth The variable names are written in CAPITALIZED letters Each variable has a specific set of attributes some of which are mandatory 3 2 1 Coordinate variables The coordinate variables orient the data in time and space For this purpose they have an axis attribute defining that they point in X Y Z and T dimensions The DEPTH variable may be positive in either upward or downward direction which is defined in its positive attribute All attributes in this section except the comment are mandatory however QC indicator may be omitted for any parameter i
24. pborne observation Mooring observation history history 2005 04 11T08 35 00Z data collected A Meyer n 2005 04 12T10 11 00Z OceanSITES file with post recovery data compiled and sent to DAC A Meyer UT Provides an audit trail for modifications to the original data It should contain a separate line for each modification with each line beginning with a timestamp and including user name modification name and modification arguments The time stamp should follow the format outlined in the note on time formats below Indicates if the file contains real time post recovery or delayed mode data The list of valid data modes is in reference table 5 quality control i quality controlz 6 Level of quality control applied to data ndicator The values are listed in reference table 2 1 quality index quality indexz A references references http www oceansites org http www noc soton ac uk animate index php A code value valid for the whole dataset 0 unknown quality A excellent no known problems regular quality checking B probably good occasional problems validation phase C extremely suspect frequent problems Published or web based references that describe the data or methods used to produceit Include a reference to OceanSITES and a project specific reference if appropriate comment comments Miscellaneous information about the data or methods used to produce it Any free format text is appro
25. pical South Atlantic Pacific Indian Ocean Southern Ocean Arctic Ocean For specific sea area use the International Hydrographic Bureau sea areas available at http vocab ndg nerc ac uk client vocabServer jsp The southernmost latitude a value between 90 and 90 degrees geospatial_lat_m geospatial_lat_max 59 8 The northernmost latitude a value between 90 and 90 degrees geospatial_lon_ geospatial_lon_min 41 2 The westernmost longitude a value between 180 and 180 i degrees geospatial_lon_ geospatial_lon_max 41 2 The easternmost longitude a value between 180 and 180 max degrees geospatial_vertic geospatial_vertical_min 10 Minimum depth for measurements al_min 0 geospatial_vertic geospatial_vertical_max 2 Maximum depth for measurements al_max 000 time coverage s time coverage start 2006 Start date of the data in UTC See note on time format below tart 03 01T00 00 00Z time coverage e time coverage end 2006 Final date of the data in UTC See note on time format below nd 03 05T23 59 29Z institution refere institution references http References to data provider institution the place to find all nces www nocs uk information on the dataset web based i e give URLs contact contact codac nocs uk Contact person s e mail author author John Smith Name of the person responsible for the creation of the dataset data_assembly_ data_assembly_center EU Data Ass
26. priate conventions OceanSITES Manual 1 1 CF 1 1 conventions netcdf_version netcdf_version 3 5 title title CIS Mooring Data summary summary Oceanographic mooring data from CIS observatory in the Central Irminger Sea North Atlantic in 2005 Measured properties temperature and salinity at ten depth levels naming authority naming authorityz OceanSl id TES idz OS CIS 1 200502 TS cdm data type cdm data type Station area North Atlantic Ocean Name of the conventions followed by the dataset Netcdf version used for the data set Free format text describing the dataset The display of these two attributes together should allow data discovery for a human reader title title of the dataset Use the file name if in doubt summary a longer description of the dataset A paragraph of up to 100 words is appropriate The id and naming authority attributes are intended to provide a globally unique identification for each dataset For OceanSITES data use naming authorityz OceanSITES and id file name without nc suffix which is designed to be unique The cdm data type attribute gives the Unidata CDM common data model data type used by THREDDS E g Point Trajectory Station Radial Grid Swath Use Station for OceanSITES mooring data More http www unidata ucar edu projects THREDDS CDM CDM TDS htm Geographical coverage Try to compose of the following North Tro
27. specified whether in attributes or separate variables which are outlined in the notes below the table The variable names are standardized in reference table 3 replace lt PARAM gt with any of the names indicated there Mandatory attributes are marked as such however OceanSITES requests that all other attributes be used and contain meaningful information unless technical reasons make this impossible Type Name Dimension Attributes Float lt PARAM gt TIME DEPTH PARAM long name Y PARAMs standard name lt X gt lt PARAMS gt units lt Y gt lt PARAM gt _ FillValue Y lt PARAM gt QC_indicator lt X gt PARAM QC procedure X PARAM valid min Y PARAM valid max Y lt PARAM gt comment lt Y gt lt PARAM gt sensor_depth Y lt PARAM gt ancillary_variables lt Y gt lt PARAM gt uncertainty Y lt PARAM gt accuracy Y lt PARAM gt precision lt Y gt PARAM resolution Y lt PARAMs gt cell methods lt Y gt lt PARAM gt DM_indicator lt Y gt Comment Contains data values PARAM names are defined in reference table 3 Exampes TEMP PSAL DOXY These 3 attributes are mandatory standard_name units and FillValue The others attributes are highly recommended if available lt X gt standardized attributes listed in reference tables Y attributes whose value is set by the PI Principal
28. the GDAC e There is a header section lines of which start with characters e The information sections are comma separated values e Each line contains the following information e FILE the file name beginning from the GDAC root directory DATE UPDATE the update date of the file YY Y Y MM DDTHH MESSZ e START DATE first date for observations YY Y Y MM DDTHH MESSZ e END DATE last date for observations Y Y Y Y MM DDTHH MESSZ e SOUTHERN MOST LATITUDE e NORTHERN MOST LATITUDE e WESTERN MOST LONGITUDE EASTERN MOST LONGITUDE e UPDATE INTERVAL M monthly D daily Y yearly V void e SIZE the size of the file in megabytes The fill value is empty eg GDAC data files index oceansites files index txt OceanSites FTP GLOBAL INDEX ftp ftp ifremer fr ifremer oceansites Contact http Awww oceansites org Index update date YYYY MM DDTHH MI SSZ 2008 03 30T 18 37 46Z FILE DATE_UPDATE START_DATE END_DATE SOUTHERN_MOST_LATITUDE NORTHERN_MOST_LATITUDE WESTERN_MOST_LONGITUDE EASTER N_MOST_LONGITUDE UPDATE_INTERVAL SIZE TAO 0n170w OS 0n170w SW LW 2m nc 2008 04 12T08 05 00Z 2007 03 17T18 07 00Z 2008 04 12T08 05 00Z 0 0 170 170 M 16 7
29. ttribute lt PARAM gt uncertainty if it is constant or in a variable of its own lt PARAM gt _UNCERTAINTY if it is not constant If uncertainty is given in either way the attribute lt PARAM gt accuracy is optional If it is impossible to estimate the overall measurement uncertainty it is required to define at least the attribute lt PARAM gt accuracy with the nominal sensor accuracy The attributes lt PARAM gt precision and PARAM resolution are optional they contain the sensor precision and resolution if defined Note on data modes DM Data mode may be represented as a global attribute data mode if all data is a single mode or as an attribute to a variable lt PARAM gt DM_indicator if all data for lt PARAM gt is in a single mode If a parameter contains a mixture of modes these attributes should be set to M and the actual data modes should be represented by an extra variable lt PARAM gt _DM The values for the data modes are explained in reference table 5 Example for sea temperature measurements and associated quality flags Float TEMP TIME LEVEL TEMP long name sea water temperature in situ ITS 90 scale TEMP standard_name sea water temperature TEMP units degree Celsius TEMP FillValue 99999 f TEMP QC indicator 1 TEMP valid min 2 0f TEMP valid max 40 f TEMP comment TEMP ancillary variables TEMP QC TEMP resolution 0 001f TEMP uncertainty 0 01f TEM
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