guidelines for submitting data from odv surveys to the ... for... · odv is a common data transport...

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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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

http://www.ocean.org.il/

mailto:[email protected]?subject=ISRAMAR%20Data%20Transport%20Formats








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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


http://isramar.ocean.org.il/isramar2009/

http://isramar.ocean.org.il/perseus_data/TextTemplates/Convertors/Data_Template.zip



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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)


http://isramar.ocean.org.il/perseus_data/Default.aspx

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


Bot. Depth [m] — Bathymetric water depth in meters where the sample was collected or


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.


http://isramar.ocean.org.il/perseus_data/DataFormat.aspx

https://www.bodc.ac.uk/data/codes_and_formats/odv_format/



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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.


http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=C17

http://seadatanet.maris2.nl/v_edmo/welcome.asp


http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=l08



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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])


http://odv.awi.de/fileadmin/user_upload/odv/misc/odv4Guide.pdf





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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


http://localhost:62765/WebSite/DownloadFile.aspx

http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P01



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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


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




16

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






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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://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=L20




18

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.




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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.




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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:


http://isramar.ocean.org.il/perseus_data/DataSubmittion.aspx

http://isramar.ocean.org.il/perseus_data/Register.aspx



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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”.




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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:


http://isramar.ocean.org.il/perseus_data/DataManagement.aspx



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