Status of tests with handling marine biological data in SeaDataNet - follow-up of SeaDataNet Deliverable 8.4
TTT 19-20 March 2014
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Deliverables• D8.4a Analysis report with required adaptions for
marine biological data• D8.4b Format documentation• Example files
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D8.4a Analysis report• Analysis
– Types of data– Data use and applications– Standards and practices in the biological community– Requirements– Required adaptations of SeaDataNet infrastructure
• Data transport format• Towards operational data exchange
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D8.4b Format documentation• Format:
– CDI metadata– ODV biology variant
• Mandatory fields (8 + 10)• Optional fields: P01 & P06 terms• Semantic header
• Version: BioODV_1.0
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Example files• Types
– Grab/core benthos community data with density and biomass values.
– Zooplankton community with samples from different depths
– Demersal fish population data with densities for different size classes and individual fish measurements (examples of subsamples are included)
– Pollutant concentrations in biota specimens
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Testing and feedback• Feedback from ICES
– feedback 01/11/2013: 3 comments• Core biological information i.e min/max depth only
available in the linked CDI might be problematic. ODV files should be self-describing.
• Main focus on biological community data and to a lesser extent on contaminants data.
• Contaminant data require separate field for describing compounds
• Testing on IMARES trawl data good starting point
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EMODnet biology• Data flow
– Web Feature Services (WFS)– Integrated Publishing Toolkit (IPT)– Custom REST services– SDN -> IFREMER will test
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Testing and feedback• Feedback from IFREMER
– feedback 02/12/2013: 3 comments; clarified/resolved• Some mandatory fields could be problematic unless the "Unknown" (or
something equivalent) value is permitted. Do you confirm this is the case for the "LifeStage" and the "ObservedIndividualCount" fields ?
• What would be the value of the SamplingEffort field in the case the only information we have is the sampling position?
• If no subsampling occurred (then the SubSamplingCoefficient=1, right ?) may the "SubsampleID" be the same as the "SampleID" ?
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Testing and feedback• Feedback from IFREMER
– feedback 19/03/2014:• Appreciation for most of variants specific of biology files, especially to indicate
the taxon without use a P01 code per taxon. Using the scientific name (WoRMs) and the Aphia ID is ok for us.
• # Mandatory fields that will be empty
• Testing status: preparing phytoplankton data for delivery
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Testing and feedback• Feedback from IMARES/NIOZ (WaLTER project)
– feedback 18/09/2013: 11 comments; clarified/resolved– feedback 13/11/2013: 4 comments; clarified/resolved– feedback 18/03/2014: 6 comments:
• “Genus sp.” -> in WoRMS just “Genus”• Both ScientificName and AphiaID needed?• SubsampleID en Subsampling coefficient required?• LifeStage list available?• Parts of organisms -> 0.1 individual OK?• Backward compatibility?
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Testing and feedback• Testing status: first ODV bio files created
– 12 CDI files for validation at MARIS (1970)– 582 files ready at IMARES/NIOZ for publishing at DM
(1970-2013)
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Developments needed
• Ocean Data Viewer– Incorporate information from CDI– Aggregate single localCDI data files– Develop appropriate filtering and visualisation tools
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Developments needed
ODVBio
Machine-2-m
achine interface
Data provider
Tools to be developed/adapted
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