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Templates for Nutrients, Dissolved Gases, and Contaminants in Various Matrices

This document provides information and examples of data templates for nutrients, dissolved gases, and contaminants in water, sediment, and biota matrices. It utilizes SeaDataNet infrastructure and standards for data exchange.

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Templates for Nutrients, Dissolved Gases, and Contaminants in Various Matrices

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  1. ODV format templates for nutrients, dissolved gases and contaminants in different matrixes (water, sediment, biota) OGS – Marina Lipizer EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  2. EMODnet Chemistry usesSeaDataNet infrastructure for the technical set-up. • It adopts: • SeaDataNet Standards(SDN) for data and metadata, and for product data and metadata • Common Data Index mechanism(CDI) to access data with data policy • Ocean Data View format (ODV) for data exchange https://www.seadatanet.org/ EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  3. Data Templates Information and examples of Data transport formats: https://www.seadatanet.org/Standards/Data-Transport-Formats EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  4. Current information available: • Templates for dataset on: • Vertical profiles • Time series • Water • Sediment (?) • Biota (?) http://www.seadatanet.org/Standards-Software/Data-Transport-Formats EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  5. Data Templates Templates of datasets for water column data (eg. Nutrients, dissolved oxygen, contaminants: ODV_timeseries_chemical_data.txt ODV_vertical_profiles_CTD_with_instruments.txt BioODV_1.0d.xls EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  6. Data Templates DistinctionbetweenVERTICAL PROFILES and TIME-SERIES: • Vertical profiles: • Profile data have row_groups made up of measurements at different depths. The primary variable (which is indicated in column 10) is the ‘z co-ordinate’, which is either depth in metres or pressure in decibars. • Used for stationsusuallynotrepeatedregularly over time, for whichseveraldepths are sampled. Typicalexamples: • CTD profiles, bottlestations (chemical data, chlorophyll, plankton,…) 1 2 3 4 5 6 7 8 9 10 11 12 …. …. EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  7. Data Templates • Time series: • Point time series have row_groups made up of measurements from a given instrument at different times. The primary variable (column 10) is time. • Usedfor the same station repeatedregularly over time, for whichusually a single depthissampled. Typicalexamples: • biotacomposition (contaminants in biota), sedimentcomposition, mooring data (eg. oceanographicbuoy) Example: Time series of bottle data 1 2 3 4 5 6 7 8 9 10 11 12 …. …. EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  8. Guidelines for sediment data Examples of samplingdevices The «depth» variablerepresents a depth INSIDE the seabed. P01: COREDIST: The distance of a sensor or sampling point below the floor of a water body a b c d COREDIST a: Grab; b: box core; c: core (single); d: multicore EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  9. Guidelines for sediment data Samplingdevice: core Whichdepth? EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  10. Guidelines for sediment data Additional depth information. Particular cases: Core cut into sections: MINCDIST: http://vocab.nerc.ac.uk/collection/P01/current/MINCDIST/ - The distance between the top of a core sample and the seabed. MAXCDIST: http://vocab.nerc.ac.uk/collection/P01/current/MAXCDIST/ - The distance between the base of a core sample and the seabed. For an unsegmented core with its top coincident with the bed this is equivalent to the core length (MAXCDIST*) COREDIST: http://vocab.nerc.ac.uk/collection/P01/current/COREDIST/ - The distance of a sensor or sampling point below the floor of a water body SEGMLENG: http://vocab.nerc.ac.uk/collection/P01/current/SEGMLENG/ - The physical length of a sample upon which measurements have been made As a general rule: COREDIST = MINCDIST + (MAXCDIST-MINCDIST)/2 and SEGMLENG = MAXCDIST - MINCDIST. EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  11. Guidelines for sediment data Seabed MINCDIST Samples from an entire, unsegmented core: COREDIST SEGMLENG sediment MAXCDIST MINCDIST: http://vocab.nerc.ac.uk/collection/P01/current/MINCDIST/ - The distance between the top of a core sample and the seabed. * For an unsegmented core with its top coincident with the bed this is 0. MAXCDIST: http://vocab.nerc.ac.uk/collection/P01/current/MAXCDIST/ - The distance between the base of a core sample and the seabed. *For an unsegmented core with its top coincident with the bed this is equivalent to the core length COREDIST: http://vocab.nerc.ac.uk/collection/P01/current/COREDIST/ - The distance of a sensor or sampling point below the floor of a water body SEGMLENG: http://vocab.nerc.ac.uk/collection/P01/current/SEGMLENG/ - The physical length of a sample upon which measurements have been made EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  12. Guidelines for sediment data • Depth information: • Mandatory: COREDIST • Optional (stronglyrecommended): MAXCIDST, MINCDIST • Optional: SEGMLENG • Vertical profiles: • Primaryvariableis COREDIST • Time series: • Primaryvariableis TIME EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  13. Examples of P01 Concentration of contaminants in the sediment: When information on size class is indicated: When information on size class is indicated or not: EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  14. Examples of P01 Reach the correct P01 from P02: Discovery vocabulary: Scroll the list to find the correct P01 (other examples at the end) EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  15. Templates for sediment data Vertical profiles: Time series: Templates from Geo Seas Project and SDN http://www.geoseas.eu/ EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  16. Biota Templates Guidelines for biotacomposition (eg. contaminants in biota) data: Time series (mostly): Point time series have row_groups made up of measurements at different times. The primary variable is time. EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  17. Open issues: • Selection of Time – seriesvs Vertical Profileissometimestricky and subjective in case of repeatedprofiles over time or time-seriesatseveraldepths EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  18. Examples of P01 Scroll the list to find the correct P01 (other examples at the end) EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

  19. Examples of P01 Scroll the list to find the correct P01 (other examples at the end) EMODnet Chemistry 3 Kick-Off meeting, 17-19 May 2017

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