status of tests with handling marine biological data in seadatanet - follow-up of seadatanet...

Status of tests with handling marine biological data in SeaDataNet - follow-up of SeaDataNet Deliverable 8.4

TTT 19-20 March 2014

[email protected] – www.seadatanet.org

Deliverables• D8.4a Analysis report with required adaptions for

marine biological data• D8.4b Format documentation• Example files


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


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


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


Example files

• Mqlkdsjmlqkdj• Mlqkdmqlkdkfj


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


EMODnet biology• Data flow

– Web Feature Services (WFS)– Integrated Publishing Toolkit (IPT)– Custom REST services– SDN -> IFREMER will test


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" ?


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


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?


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)


Developments needed

• Ocean Data Viewer– Incorporate information from CDI– Aggregate single localCDI data files– Develop appropriate filtering and visualisation tools


Developments needed

ODVBio

Machine-2-m

achine interface

Data provider

Tools to be developed/adapted

status of tests with handling marine biological data in seadatanet - follow-up of seadatanet...

Documents

feedback feedback

developedadapted slide

delivery slide

phytoplankton data

contaminants data

contaminant data

ifremer feedback

biological community