Guidelines for Submitting Data from ODV Surveys to the ... for... · ODV is a common data transport...
Transcript of Guidelines for Submitting Data from ODV Surveys to the ... for... · ODV is a common data transport...
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Guidelines for Submitting Data from ODV Surveys to the National Archive at the Israel Oceanographic & Limnological
Research Center (IOLR)
ISRAMAR Data Transport Formats
History
Version Authors Date Comments
1 Isaac Gertman Yevgeniya Krivenko
2013-06-23 Initial ODV format description.
2 Isaac Gertman Yevgeniya Krivenko Tal Ozer Boris Katsnelson
2013-10-21 Excel template file added. Online Data Submission added. Common Vocabularies version updated to new NVS2.0.
Content
History ........................................................................................................................................................... 1
Content ......................................................................................................................................................... 1
Introduction .................................................................................................................................................. 2
Ocean Data View format (ODV) .................................................................................................................... 4
Format ....................................................................................................................................................... 4
Data mapping ............................................................................................................................................ 5
Parameters mapping in ODV file ............................................................................................................... 5
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Metadata formats ......................................................................................................................................... 7
Optional metadata header .................................................................................................................... 8
Optional metadata columns ................................................................................................................. 9
Codes and vocabularies .............................................................................................................................. 10
Parameters .......................................................................................................................................... 10
Units .................................................................................................................................................... 16
Quality flags ........................................................................................................................................ 16
Data availability ................................................................................................................................... 17
Links to online vocabularies interfaces ............................................................................................... 17
Excel template file ....................................................................................................................................... 17
Metadata editing ................................................................................................................................ 18
Data editing ......................................................................................................................................... 18
Quality flagging ................................................................................................................................... 19
Export to ODV ..................................................................................................................................... 19
Online Data Submission .............................................................................................................................. 20
Introduction
Israel Marine Data Center (http://isramar.ocean.org.il/isramar2009/) maintains a database (DB) with
multi parametric vertical profile data since 2001. The DB contains vertical profiles of physical (excluding
XBT data), chemical and biological parameters observed from research vessels and autonomous
platform in Mediterranean and Black Seas.
ISRAMAR accepts data from data providers in a standard format (ODV). ISRAMAR provides EXCEL base
convertor to ODV. This document contains detailed instructions for data submission:
1. EXCEL data table template download
2. Fill data in the EXCEL table
3. Automatic conversion to ODV format text file
4. Online ODV file submission
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ISRAMAR provides consultation for data submission process.
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Ocean Data View format (ODV)
ISRAMAR supports ODV data format for online data submission.
This online data management system was approved and tested in PERSEUS (Policy-Oriented Marine
Environmental research In the Southern European Seas) on-going project:
http://isramar.ocean.org.il/perseus_data/Default.aspx
ODV is a common data transport format for profiles, time series and trajectories, recommended by Pan-
European Infrastructure for Ocean & Marine Data Management in the frame of SeaDataNet project and
accepted by more than 600 scientific data collecting laboratories from governmental organizations and
private industry in the countries bordering the European seas.
This format is an ASCII text file with tab separated observation values, station metadata and parameters
list. The file extension is .txt, however it can be easily opened and managed in MS Excel.
In order to help data providers with ODV files generation, ISRAMAR developed a simple MS Excel data
file template with automatic convert to ODV option. Please read more in “Excel template file”
paragraph.
Format
The data format follows that of a spreadsheet — a collection of rows (comment, column header and
data) with each data row having the same fixed number of columns. ODV file contains
Parameters mapping component
Metadata columns
Data columns — two columns per variable (value and flag)
Data rows containing exactly the same parameters grouped together — known as 'stations'.
The format includes standard codes which are listed below in “Codes and vocabularies” paragraph.
Example (the full ODV example can be downloaded here:
http://localhost:62765/WebSite/TextTemplates/ODV4_Example.txt)
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Data mapping
Data of different 'shape' (profile, time series and trajectory) are mapped into the spreadsheet as follows
Profile data — CTD and bottle data
Stations are made up of measurements at different depths, with the metadata date/time set to
be the start of the profile. The primary variable is the 'z coordinate' which can be either depth in
meters or pressure in decibars. The rows within the station are ordered by increasing depth.
Point time series — current meter or sea level data
Stations are made up of measurements from a given instrument at different times, with the
metadata date/time set to the start of the measurements. The primary variable is time (UT)
encoded as
Chronological Julian Date [days]
Defined as the time elapsed in days from 00:00 on 01 January 4713 BC.
Rows within the station are ordered by increasing time, with the 'z coordinate' (instrument depth) —
essential for many types of data — stored as a data variable.
Trajectories — underway data
Stations are made up of a single measurement making the metadata time and positions the
spatio-temporal coordinate channels. The primary variable is the 'z coordinate' standardized as
depth in meters. Rows within the file are ordered by increasing time.
Parameters mapping in ODV file
Each file consists of three components, namely
1. Comment rows
a. User comments
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These are prefixed by the characters // and may appear anywhere in the data file. Comment
records are used to enrich the data files with additional usage metadata. The first row in ODV
files supplied by BODC contains a URL to our data documentation.
b. Parameters mapping header
These are mandatory comment lines. Their function is to map the text strings used to
label the metadata and data columns to standardized SeaDataNet concepts —
necessary if data files from different sources are to be combined in a meaningful way.
The header begins with the line: //SDN_parameter_mapping. This is followed by a line
for each data column (including the primary variable) made up from three parts —
tagged to look like an XML element.
Subject — Contains the text used to label the column EXACTLY as it appears in
the column row header WITHOUT the units declaration, prefixed by
'SDN:LOCAL:' to encode it as a SeaDataNet URN.
Object — Contains the URN to a concept from the SeaDataNet controlled
vocabulary P01.
Units — Contains a URN for the storage units for the data column used IN THE
FILE from the SeaDataNet controlled vocabulary P06.
2. Column header row
The header row contains a label for each column of the file. They are presented (from the left)
as standardized metadata, followed by column pairs (data plus a qualifying flag) for the primary
variable and the data parameters. The first heading in each pair is the description for the data
parameter plus its storage units enclosed in brackets, for example 'Current Dir [deg T]', with the
second always being 'QV:SEADATANET' or 'QF'.
3. Data rows
The metadata columns are populated as follows
Cruise — A text string identifying the grouping label for the data object to which the data row
belongs. Obviously the cruise name for data types such as CTD and bottle data, but may be a
mooring name for current meter data.
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Station — A text string identifying the data object to which the data row belongs. This will be
the station name for some types of data, but could also be an instrument deployment identifier.
Type — The type of data. Set to 'C' for CTD and XBT profile data and 'B' for bottle profile data.
For time series and trajectories set to 'B' for small (<250) row groups or 'C' for larger row groups.
yyyy-mm-ddThh:mm:ss.sss — Date and time (UT) when the sample was collected or
measurement was made in extended ISO8601 format — 2008-04-23T15:15:00.000.
Longitude [degrees_east] — Longitude (decimal degrees) where the sample was collected or
measurement was made.
Latitude [degrees_north] — Latitude (decimal degrees) where the sample was collected or
measurement was made.
Bot. Depth [m] — Bathymetric water depth in meters where the sample was collected or
measurement was made.
These are followed by the primary variable value, its flag and then the data value plus qualifying
flag pairs for each parameter. If there is no data value then the data value column is left blank
with the flag field set to '9' - missing value.
More information about data exchange format supported for online data submission:
http://isramar.ocean.org.il/perseus_data/DataFormat.aspx
Detailed information about ODV format:
https://www.bodc.ac.uk/data/codes_and_formats/odv_format/
Metadata formats
In addition to station metadata described in ODV format above, metadata of the dataset required for
data submission into ISRAMAR DB:
Dataset name — Text string identifying the set of data in submission.
Project — Text string identifying the project.
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Ship — ICES code from Platform Codes (C17) vocabulary. In case of the time series and
trajectory observations, the “Unknown” ship code can be set.
Data Center —EDMO code from European Directory of Marine Organisations vocabulary. For
example: EDMO code for Ministry of Energy and Water Resources is 3004.
Country — ISO code from International Standards Organisation countries (C32) vocabulary. For
example: Israel code is IL.
Availability — SDN code from SeaDataNet Data Access Restriction Policies Access (L08)
vocabulary.
There is user friendly interface in the online data submission system, which helps to find needed
ship/data center/country by name.
For easier data submission, the metadata values will be automatically loaded into the online metadata
interface from header addition to the ODV format or from optional metadata columns.
Dataset name will be automatically loaded from file name and can be edited in online metadata
interface.
Access to each dataset should defined by the data provider manually during the data submission
procedure.
Optional metadata header
If ship, country and data center metadata is common for all samples in the file, it can be mentioned once
in Cruise Metadata part. It should be in commented lines with following XML tags at the top of ODV file.
<rpOrgName> tag — represents data originator institute. SDNIdent attribute with value as
SDN:EDMO: + institute EDMO code is required for this tag.
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(Ex.: <rpOrgName SDNIdent="SDN:EDMO::963"> Israel Oceanographic and Limnological
Research (IOLR) </rpOrgName>)
<dataType> tag — represents instrument type. SDNIdent attribute with value as SDN:C77: +
type BODC code is required for this tag.
(Ex.: <dataType SDNIdent="SDN:C77::H09"> Water bottle stations </dataType>)
<platform> tag — represents ship. SDNIdent attribute with value as SDN:C17: + ship ICES code
code is required for this tag.
(Ex.: <platform SDNIdent="SDN:C17::47SK"> Shikmona </platform>)
<country> tag — represents country. SDNIdent attribute with value as SDN:C32: + country ISO
code is required for this tag.
(Ex.: <country SDNIdent="SDN:C32::IL"> Israel </country>)
<project> tag — represents project name.
(Ex.: <project> PERSEUS </project>)
Optional metadata columns
Ship, country and data center metadata can be included in METAVAR columns of ODV formatted file.
Metadata columns names may have qualifiers of the form :METAVAR:TEXT:<valueBytes>, where
<valueBytes> is the maximum length of the value + 1.
The following columns may be automatically loaded into the online metadata interface:
EDMO_code — represents data originator institute. Value is an EDMO code from European
Directory of Marine Organisations vocabulary.
Ship:METAVAR:TEXT: <valueBytes> — represents ship. The value is a ship name string.
(Ex.: Shikmona)
(Ex. Including ICES code: Shikmoma [SDN:C17::47SK])
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Country:METAVAR:TEXT: <valueBytes> — represents country. The value is a country name
string.
(Ex.: Israel)
(Ex. Including ISO code: Israel [SDN:C32::IL])
Codes and vocabularies
The entire list of all codes can be found in supported ISRAMAR_Vocabs.mdb, available at
http://localhost:62765/WebSite/DownloadFile.aspx.
The parameters lists below defined by suggestion from Ministry of Environmental Protection for marine
data monitoring with mapping to accepted standard codes.
Parameters
Mapped to BODC Parameter Usage vocabulary (P01)
Seawater CTD Parameters List
Param Name P01 Code Description
Pressure [db] PRESPR01
Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level
Temperature [deg C] TEMPPR01 Temperature of the water body
Salinity [PSU] PSALZZXX Practical salinity of the water body by computation using UNESCO 1983 algorithm
Ph [pH units] PHXXZZXX pH per unit volume of the water body
Turbidity [NTU] TURBXXXX Turbidity of the water body
{O2} Concentration [umol/l] DOXYZZXX
Concentration of oxygen {O2} per unit volume of the water body [dissolved phase]
{O2} Saturation [%] OXYSZZ01 Saturation of oxygen {O2} in the water body [dissolved phase]
Fluorescence FLUOZZZZ Fluorescence of the water body
Seawater Bottle Parameters List
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Param Name P01 Code Description
Pressure [db] PRESPR01
Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level
TOC [µmol/L] MDMAP011 Concentration of carbon (total) per unit volume of the water body [particulate phase]
TSS [g/m^3] TSEDZZZZ Concentration of suspended particulate material {SPM} per unit volume of the water body
Turbidity [NTU] TURBXXXX Turbidity of the water body
Chl-a [ug/l] CHLTVOLU Concentration of chlorophyll per unit volume of the water body
NO3+NO2 [µmol/L] NTRZYYDZ
Concentration of nitrate+nitrite {NO3+NO2} per unit volume of the water body [dissolved plus reactive particulate phase]
Ammonium [µmol/L] AMONZZXX Concentration of ammonium {NH4} per unit volume of the water body [unknown phase]
Nitrogen [µmol/L] NTOTZZXX Concentration of nitrogen (total) per unit volume of the water body [dissolved plus reactive particulate phase]
Phosphorus [µmol/L] TPHSDSZZ
Concentration of phosphorus (total) per unit volume of the water body [dissolved plus reactive particulate <unknown phase]
Radium-228 [mBq/l] RAD228WC
Activity of radium-228 {228Ra} per unit volume of the water body [dissolved plus reactive particulate <1um phase] by filtration, Mn absorption and gamma spectroscopy
Radium-226 [mBq/l] RAD226WC
Activity of radium-226 {226Ra} per unit volume of the water body [dissolved plus reactive particulate <1um phase] by filtration, Mn absorption and gamma spectroscopy
Zn [nmol/l] RWS00028 Concentration of zinc {Zn} per unit volume of the water body [dissolved plus reactive particulate phase]
Sb [nmol/l] RWS00031 Concentration of antimony {Sb} per unit volume of the water body [dissolved plus reactive particulate phase]
Pb [nmol/l] PBUFWC02 Concentration of lead {Pb} per unit volume of the water body [dissolved plus reactive particulate phase]
Ni [nmol/l] RWS00027 Concentration of nickel {Ni} per unit volume of the water body [dissolved plus reactive particulate phase]
Hg [nmol/l] HGUFWC02 Concentration of mercury {Hg} per unit volume of the water body [dissolved plus reactive particulate phase]
Fe [nmol/l] RWS00033 Concentration of iron (total) {Fe} per unit volume of the water body [dissolved plus reactive particulate phase]
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Cu [nmol/l] CUUFWC02 Concentration of copper {Cu} per unit volume of the water body [dissolved plus reactive particulate phase]
Cr [nmol/l] CRUFWC02 Concentration of chromium {Cr} per unit volume of the water body [dissolved plus reactive particulate phase]
Cd [nmol/l] CDUFWC02 Concentration of cadmium {Cd} per unit volume of the water body [dissolved plus reactive particulate phase]
Be [nmol/l] RWS00030 Concentration of beryllium {Be} per unit volume of the water body [dissolved plus reactive particulate phase]
Ba [nmol/l] RWS00029 Concentration of barium {Ba} per unit volume of the water body [dissolved plus reactive particulate phase]
As [nmol/l] RWS00025 Concentration of arsenic {As} per unit volume of the water body [dissolved plus reactive particulate phase]
Al [nmol/l] ALPICP01
Concentration of aluminium {Al} per unit volume of the water body [particulate >1um phase] by acid leaching of filter residue and inductively-coupled plasma mass spectrometry
V [nmol/l] RWS00042 Concentration of vanadium {V} per unit volume of the water body [dissolved plus reactive particulate phase]
Alkalinity [mEquiv/l] ALKYZZXX Total alkalinity per unit volume of the water body
TPH [ug/l] TPHUFWAT
Concentration of total petroleum hydrocarbons {TPH} per unit volume of the water body [dissolved plus reactive particulate phase]
Naphthalene RWS00110
Concentration of naphthalene {CAS 91-20-3} per unit volume of the water body [dissolved plus reactive particulate phase]
Acenaphthylene CPAHWC04
Concentration of acenaphthylene {CAS 208-96-8} per unit volume of the water body [dissolved plus reactive particulate phase] by gas chromatography-mass spectrometry
Acenaphthene CPAHWC03
Concentration of acenaphthene {CAS 83-32-9} per unit volume of the water body [dissolved plus reactive particulate phase] by gas chromatography-mass spectrometry
Fluorene CPAHWC13
Concentration of fluorene {CAS 86-73-7} per unit volume of the water body [dissolved plus reactive particulate phase]
Anthracene ANUFWC02
Concentration of anthracene {CAS 120-12-7} per unit volume of the water body [dissolved plus reactive particulate phase]
Phenanthrene CPAHWC16
Concentration of phenanthrene {CAS 85-01-8} per unit volume of the water body [dissolved plus reactive particulate phase] by gas chromatography-mass spectrometry
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Fluoranthene FLUFWC02
Concentration of fluoranthene {CAS 206-44-0} per unit volume of the water body [dissolved plus reactive particulate phase]
Pyrene CPAHWC02
Concentration of pyrene {CAS 129-00-0} per unit volume of the water body [dissolved plus reactive particulate phase]
Benz(a)anthracene CPAHWC06
Concentration of benz(a)anthracene {CAS 56-55-3} per unit volume of the water body [dissolved plus reactive particulate phase]
Chrysene CPAHWC11
Concentration of chrysene {CAS 218-01-9} per unit volume of the water body [dissolved plus reactive particulate phase]
Benzo(b)fluoranthene CPAHWC08
Concentration of benzo(b)fluoranthene {CAS 205-99-2} per unit volume of the water body [dissolved plus reactive particulate phase]
Benzo(k,j)fluoranthene CPAHWC10
Concentration of benzo(k)fluoranthene {CAS 207-08-9} per unit volume of the water body [dissolved plus reactive particulate phase]
Benzo(a)pyrene CPAHWC07
Concentration of benzo(a)pyrene {CAS 50-32-8} per unit volume of the water body [dissolved plus reactive particulate phase]
Indeno(1,2,3-c,d)pyrene CPAHWC14
Concentration of indeno(1,2,3-cd)pyrene {CAS 193-39-5} per unit volume of the water body [dissolved plus reactive particulate phase]
Dibenz(a,h)anthracene CPAHWC12
Concentration of dibenzo(a,h)anthracene {CAS 53-70-3} per unit volume of the water body [dissolved plus reactive particulate phase]
Benzo(g,h,i)perylene CPAHWC09
Concentration of benzo(g,h,i)perylene {CAS 191-24-2} per unit volume of the water body [dissolved plus reactive particulate phase]
Sediment Parameters List
Param Name P01 Code Description
Bottom Pressure [db] PRESPR01
Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level. For sediments, this parameter shows the pressure on the bottom.
TOC [%] TCCNXXXX Concentration of carbon (total) per unit dry weight of sediment
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Radium-226 [Bq/kg] R226GSXT Activity of radium-226 {226Ra} per unit dry weight of sediment by gamma spectroscopy
Thorium-228 T228GSPS
Activity of thorium-228 {228Th} per unit dry weight of suspended particulate material by sediment trapping and gamma spectroscopy
Zn [mg/kg] MZNSP012 Concentration of zinc {Zn} per unit dry weight of sediment
Sb [mg/kg] SBCNICXT Concentration of antimony {Sb} per unit dry weight of sediment by inductively-coupled plasma mass spectrometry
Pb [mg/kg] MPBSP012 Concentration of lead {Pb} per unit dry weight of sediment
Ni [mg/kg] MNISP012 Concentration of nickel {Ni} per unit dry weight of sediment
Hg [mg/kg] MHGSP012 Concentration of mercury {Hg} per unit dry weight of sediment
Fe [mg/kg] MFESP012 Concentration of iron (total) {Fe} per unit dry weight of sediment
Cu [mg/kg] MCUSP012 Concentration of copper {Cu} per unit dry weight of sediment
Cr [mg/kg] MCRSP012 Concentration of chromium {Cr} per unit dry weight of sediment
Cd [mg/kg] MCDSP012 Concentration of cadmium {Cd} per unit dry weight of sediment
Be [mg/kg] SEDSBEXX Concentration of beryllium {Be} per unit dry weight of sediment
Ba [mg/kg] MBASP012 Concentration of barium {Ba} per unit dry weight of sediment
As [mg/kg] MASSP012 Concentration of arsenic {As} per unit dry weight of sediment
Al [mg/kg] MALSP012 Concentration of aluminium {Al} per unit dry weight of sediment
V [mg/kg] MVVSP012 Concentration of vanadium {V} per unit dry weight of sediment
Undecane C11 CA11GCTX
Concentration of undecan-1-ol {C11 alkanol CAS 112-42-5} per unit dry weight of sediment by gas chromatography-mass spectrometry
Dodecane C12 CA12GCTX
Concentration of dodecan-1-ol {C12 alkanol lauryl alcohol CAS 112-53-8} per unit dry weight of sediment by gas chromatography-mass spectrometry
Tetradecane C14 CA14GCTX
Concentration of tetradecan-1-ol {C14 alkanol myristyl alcohol CAS 112-72-1} per unit dry weight of sediment by gas chromatography-mass spectrometry
Hexadecane C16 CA16GCTX
Concentration of hexadecan-1-ol {C16 alkanol cetyl alcohol CAS 36653-82-4} per unit dry weight of sediment by gas chromatography-mass spectrometry
Octadecane C18 CA18GCTX
Concentration of octadecan-1-ol {C18 alkanol stearyl alcohol CAS 112-92-5} per unit dry weight of sediment by gas chromatography-mass spectrometry
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Eicosane C20 CA20GCTX
Concentration of icosan-1-ol {C20 alkanol arachidyl alcohol CAS 629-96-9} per unit dry weight of sediment by gas chromatography-mass spectrometry
Tetracosane C24 CA24GCTX
Concentration of tetracosan-1-ol {C24 alkanol lignoceryl alcohol CAS 506-51-4} per unit dry weight of sediment by gas chromatography-mass spectrometry
Octacosane C28 CA28GCTX
Concentration of octacosan-1-ol {C28 alkanol cluytyl alcohol montanyl alcohol CAS 557-61-9} per unit dry weight of sediment by gas chromatography-mass spectrometry
Dotriacontane C32 CA32GCTX
Concentration of dotriacontan-1-ol {C32 alkanol CAS 6624-79-9} per unit dry weight of sediment by gas chromatography-mass spectrometry
Hexatriacontane C36 CX36GCTX
Concentration of hexatriacontane {C36_n-alkane CAS 630-06-8} per unit dry weight of sediment by gas chromatography-mass spectrometry
TPH [ug/kg] TPHSEDXX Concentration of total petroleum hydrocarbons {TPH} per unit dry weight of sediment
Naphthalene CPAHSD15 Concentration of naphthalene {CAS 91-20-3} per unit dry weight of sediment <63um
Acenaphthylene CPAHSD04
Concentration of acenaphthylene {CAS 208-96-8} per unit dry weight of sediment <63um by gas chromatography-mass spectrometry
Acenaphthene CPAHSD03
Concentration of acenaphthene {CAS 83-32-9} per unit dry weight of sediment <63um by gas chromatography-mass spectrometry
Fluorene CPAHSD13 Concentration of fluorene {CAS 86-73-7} per unit dry weight of sediment <63um
Anthracene ANTDWT02
Concentration of anthracene {CAS 120-12-7} per unit dry weight of sediment <63um
Phenanthrene CPAHSD16 Concentration of phenanthrene {CAS 85-01-8} per unit dry weight of sediment <63um
Fluoranthene CPAHSD01
Concentration of fluoranthene {CAS 206-44-0} per unit dry weight of sediment <63um by gas chromatography-mass spectrometry
Pyrene CPAHSD02 Concentration of pyrene {CAS 129-00-0} per unit dry weight of sediment <63um
Benz(a)anthracene CPAHSD06 Concentration of benz(a)anthracene {CAS 56-55-3} per unit dry weight of sediment <63um
Chrysene CPAHSD11 Concentration of chrysene {CAS 218-01-9} per unit dry weight of sediment <63um
Benzo(b)fluoranthene CPAHSD08 Concentration of benzo(b)fluoranthene {CAS 205-99-2} per unit dry weight of sediment <63um
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Benzo(k,j)fluoranthene CPAHSD10
Concentration of benzo(k)fluoranthene {CAS 207-08-9} per unit dry weight of sediment <63um
Benzo(a)pyrene CPAHSD07 Concentration of benzo(a)pyrene {CAS 50-32-8} per unit dry weight of sediment <63um
Indeno(1,2,3-c,d)pyrene CPAHSD14
Concentration of indeno(1,2,3-cd)pyrene {CAS 193-39-5} per unit dry weight of sediment <63um
Dibenz(a,h)anthracene CPAHSD12
Concentration of dibenzo(a,h)anthracene {CAS 53-70-3} per unit dry weight of sediment <63um
Benzo(g,h,i)perylene CPAHSD09 Concentration of benzo(g,h,i)perylene {CAS 191-24-2} per unit dry weight of sediment <63um
Units
Units by BODC Data Storage Units vocabulary (P06)
Unit name P06 Code Description
mEquiv/l MEQL MilliEquivalents per litre
g/m^3 UGMC Grams per cubic metre
degC UPAA Degrees Celsius
ppt UPPT Parts per thousand
USPC Not specified
ug/kg UUKG Micrograms per kilogram
pH units UUPH pH units
Quality flags
Quality flags by SeaDataNet measuring qualifier flags vocabulary (L20)
L20 Code 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
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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9 missing value
A value phenomenon uncertain
Data availability
The following data availability flags are implemented according to SeaDataNet Data Access Restriction
Policies (L08) vocabulary:
L08 Code
Description
UN Unrestricted (free). The data are freely available to anybody and may be used for any purpose. Usage acknowledgement may be required.
RS By negotiation (restricted). The metadata regarding the cruises is open but data can be obtained on a case-by-case basis through negotiation with data provider.
OG Organization (for partners). The datasets are available to PERSEUS partners only.
Links to online vocabularies interfaces
The online codes vocabulary interfaces:
Ships: ICES Platform Codes (C17).
Country: International Standards Organisation Countries (C320)
Data Center: European Directory of Marine Organisations (EDMO)
Parameters: BODC Parameter Usage vocabulary (P01)
Units: BODC Data Storage Units vocabulary (P06)
Quality flags: SeaDataNet measuring qualifier flags vocabulary (L20)
Excel template file
Data provider can fill data in a MS Excel table and use “Convert to ODV” feature, developed by ISRAMAR
to get ready-to-submission files for his data.
The MS Excel template files can be downloaded from:
http://isramar.ocean.org.il/perseus_data/TextTemplates/Convertors/Data_Template.zip
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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Parameters list
Each template file has “Param Mapping” tab with parameters list, suggested by Ministry of
Environmental Protection for marine data monitoring.
Do not remove or rename this tab in order to keep “Convert to ODV” option available.
Metadata editing
Each template file has “Metadata” tab with list of required Meta variables related to the entire cruise,
such as data center, platform, country and project name.
Data provider is responsible to update “Description” (Column B) and “Code” (Column C) with standard
names and codes (from vocabularies list above).
“Param” (Column A) lists the XML nodes names for optional metadata header in ODV export. Do not
change this column.
Do not remove or rename this tab in order to keep “Convert to ODV” option available.
Data editing
Each template file can include multiple data tabs.
Each data tab name should starts from ‘$’ character. This name will be used as the exported ODV file
name.
The template file includes one data tab, which illustrates columns list and order:
Columns A-I are mandatory for sample metadata.
The rest of columns are parameters. This list can be edited to include more or less parameters.
Each parameter column name should be mapped to a standard code on “Param_Mapping” tab.
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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Existing values in the template file are for illustration purposes only.
Data provider is responsible to fill each data row with relevant sample metadata values and parameters
measurement values.
Automatic data import from .btl files option available on “Param_Mapping” tab -> “Import btl Files”
button.
Quality flagging
Data provider can attach data quality information to each parameter.
Update the “QF_ByExpert” (Column D) on “Param_Mapping” tab with values from “Entry Key” (Column
A) of “QF” tab.
Export to ODV
1. Ensure that the cruise metadata updated on “Metadata” tab.
2. Ensure that at least on data tab exists and its name starts from ‘$’.
3. Ensure that parameters columns names on the data tab have standard codes mapping on the
“Param_Mapping” tab.
4. Click “Convert to ODV” button on the “Param_Mapping” tab: the dropdown list of data tabs will
be enabled.
5. Choose the relevant data tab to export in ODV.
6. Check for generated ODV file in the same directory as the template file.
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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Online Data Submission
ISRAMAR supports online data submission:
http://isramar.ocean.org.il/perseus_data/DataSubmittion.aspx
There are 3 simple steps of data submission:
Pre-required step:
Login. New visitor can register online. Data provider user rights should be requested
from administrator by email: [email protected]
First step:
Upload the data file in ODV format (tab separated data file with .txt or .zip extension up
to 5 MB)
Second step:
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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Fill parameters information. Parameters names mapping to the standard codes will be
imported automatically if you use 'SDN_parameter_mapping' header as described
above.
Select “For Import” checkbox for parameters to import into ISRAMAR database.
Final step:
Fill general cruise metadata. Ship, country and data center will be imported
automatically if you use metadata header or metadata columns as described above.
If data center or ship cannot be found in the list of standard names, choose “Unknown”.
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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Data provider will receive an email report once the data import process is finished.
Data provider can manage his data through online data management interface:
Israel Oceanographic & Limnological Research Ltd. Tel-Shikmona, P.O.B. 8030, Haifa 31080 Tel: 972-4-8565200, Fax: 972-4-8511911
http://www.ocean.org.il
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