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Marine Data News Issue 39
July 2018
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In this issue of Marine Data News...

EMODnet Seabed Habitats launches a new portal 


In May 2018 EMODnet Seabed Habitats relaunched its web mapping portal providing a one-stop shop for habitat mapping data throughout Europe.

EMODnet Seabed Habitats is one of eight portals within the EMODnet initiative. The other portals cover bathymetry, geology, chemistry, physics, biology, human activities and coastal mapping. EMODnet stands for the European Marine Observation and Data Network and consists of more than 150 organisations assembling marine data, products and metadata. The aim is to make these fragmented resources more available to public and private users relying on quality-assured, standardised and harmonised marine data which are interoperable and free of restrictions on use. EMODnet is currently in its third development phase with the target to be fully deployed by 2020.
Figure 1. Screenshot of EMODnet Seabed Habitats portal
The EMODnet Seabed Habitats portal collates seabed habitat maps from survey, ground-truthing habitats point data and modelled habitat maps from across Europe. The Map Viewer is the portal’s main feature. It allows you to:

•    Interactively view map layers;
•    Download data in GIS format;
•    View metadata describing file contents; and
•    Web Mapping Services allow users to export data to personal GIS applications or other web mapping portals.

EMODnet Seabed Habitats is still actively collating data. If you have or are aware of any habitat maps from survey, modelled habitat maps or habitat point data which is not currently available through the portal then please get in touch to let us know and we can help you with the data submission process.
Visit our portal at http://www.emodnet-seabedhabitats.eu/.

If you have any suggestions for improvements to the portal or data to submit then please get in touch with us either via the online helpdesk or by emailing us at emodnetseabedhabitats@jncc.gov.uk.
MEDIN Data Archive Centres successful in gaining reaccreditation


Congratulations to the following Data Archive Centres (DACs) who have recently been successful in gaining reaccreditation as MEDIN DACs:

•    Marine Meteorological DAC (Met Office)
•    Fisheries DAC (Cefas and Marine Scotland Science

 


They gained their first accreditation as MEDIN DACs in 2011/2012. DACs are required to go through a reaccreditation process approximately every 5 years in order to ensure that they continue to meet the required standard for a MEDIN DAC.
The reaccreditation process requires the DACs to submit a form providing detailed evidence on organisational framework, quality control and maintenance, technical infrastructure, and user access and communication. The forms are then assessed by a panel of three reviewers, with accreditation completed once the feedback from the reviewers has been addressed by the DAC.



Real-time CTD data from UK research vessels assimilated into Met Office's global ocean forecasting system 

Since January 2018, the Met Office have been receiving near real time temperature and salinity profiles from the CTD (Conductivity, Temperature and Depth) instruments on board all three Natural Environment Research Council (NERC)/British Antarctic Survey (BAS) research vessels. Thanks to the hard work and perseverance of National Marine Facilities (NMF) IT technicians and scientists on board, this high quality oceanographic data is available for assimilation into the Met Office’s (Forecast Ocean Assimilation Model) FOAM system. FOAM runs daily, producing both global and regional ocean forecasts of temperature, salinity, sea-ice and currents out to seven days ahead.
Figure 2. RRS Discovery 
The on-board system works by running software that sub-samples the raw temperature and salinity values from the upcast profile at pre-defined depth levels, formats them into a text file including time and position information, and emails the file to a dedicated mailbox at the Met Office. Incoming data is processed hourly at the Met Office, where it goes through a real-time “Argo-like” QC procedure and is then formatted as a WMO TESAC (Marine observing platform extended identifier) (FM-64) message. This is ingested into the Met Office’s internal database, and is (optionally) shared on the WMO’s Global Telecommunication System (GTS), allowing other ocean forecasting centres around the world to access the data in near real time. The CTD data is usually available for assimilation within a few hours of the CTD arriving back on the ship’s deck. The system was installed on James Clark Ross in September 2014, on Discovery in October 2017, and on James Cook in January 2018. Tim Smyth (PML) is the original driving force behind the system, having written the software and installed it on James Clark Ross during an Atlantic Meridional Transect (AMT) cruise.
Figure 3. Temperature data (degrees C) from July - December 2017 collected on board RRS Discovery and assimilated into the Met Office FOAM system.
Figure 4. Temperature data (degrees C) between January-March 2018 collected on RRS James Cook
and assimilated into the Met Office FOAM system.
The sub-sampled CTD profiles are thought to be extremely high quality, at least as good as those obtained from Argo floats. The benefit over Argo data is that we receive information from wherever the ships deploy the CTD instrument, often in waters deeper than 2,000 metres, and on the continental shelves, which are too shallow, and sometimes too icy, for Argo floats to operate in. During autumn/winter 2017, RRS Discovery sent data from a north-south transect from UK to The Falklands, and from the shelf waters around South Georgia (see figure 3). RRS James Clark Ross has provided data from the Nordic Seas and the South Atlantic/Southern Ocean since July 2017 (figure 4). RRS James Cook sent data from 25-40 N and 24 S in the Atlantic during the first three months of 2018 (figure 5). 
Figure 5. Temperature data (degrees C) from July - December 2017 collected on board RRS James Clark Ross and assimilated into the Met Office FOAM system. 
We are happy to make the on-board software available to other research vessel operators. We are in the early stages of offering the software to the European research vessel fleet via EuroGOOS.

Please contact  Fiona Carse for more information.
Finding your data hard to swallow?  Streamlining JNCC's offshore data ingestion 
 
The Joint Nature Conservation Committee (JNCC) is the advisor to UK governments on nature conservation in the offshore marine environment. As part of this role JNCC carry out surveys, with our partners, of seabed habitats within Marine Protected Areas (MPAs) and beyond.  These surveys generate large quantities of data, including videos, still images, grab samples and acoustic data (collected using equipment such as multibeam echosounder (MBES) and sidescan sonar (SSS) systems). Quality checking and ingesting these data onto our network has traditionally been highly time consuming, taking many hours of staff time. These datasets can be large and complex; as such a robust and well-defined protocol is required to govern their storage, quality and management. To help tackle this issue, we have developed a semi-automated protocol, labelled 'The Offshore Survey Data Ingestion Protocol' or 'DIP', to set out a streamlined process for ingesting survey data into JNCC's data holdings. The creation of the DIP has cut our ingestion time in half. 
Figure 6. JNCC staff member Rowena Patel working on coding the ingestion processes. 
 The semi-automated processes are run through R (statistical programming language) and the DIP itself is an R markdown document (https://rmarkdown.rstudio.com/).  Some of the functions include checking for corrupt files by opening and closing files and generating a log, checking if there are any required fields that are blank and setting and checking raster values, amongst many more. We are currently developing the functions of the DIP into an R package which will be made publicly available and are working towards an automated system for exporting our data and metadata in a MEDIN compliant form for submission to the Data Archive Centres (DACs).

Development of MEDIN compliant Export Functionality for Web-Based Tool ABACUS 

Many thousands of marine biological samples are collected and analysed on an annual basis to satisfy statutory monitoring commitments (e.g. Water Framework Directive (WFD), Habitats Directive) and conditions of marine licences granted for marine activities. These include seabed samples that undergo macrobenthic, particle size distribution and chemical analysis, water samples analysed to monitor planktonic communities and scientific trawl samples to assess fish and other mobile species. 

Figure 7. Preamble provided with all MEDIN compliant data exports from ABACUS describing how the data is generated and the process in which it can be easily archived with a MEDIN Data Archive Centre (DAC).
Despite the requirement for these analytical processes to be conducted by laboratories participating in recognised quality control schemes (e.g. the NE Atlantic Marine Biological Quality Control (NMBAQC) scheme), there remains fundamental issues surrounding the recording of non-standardised marine biological data. These issues stem from inter-analyst and inter-laboratory variability in sample analysis methodologies, recording practices, species naming, the use of taxonomic qualifiers and so on.

To address this ever-apparent issue, MEDIN partner Ocean Ecology Limited (OEL) have developed a web-based platform (ABACUS) for marine scientists to record, quality assure, store and export standardised marine biological data. Through support from MEDIN’s Small Data Archiving Project initiative, a bespoke export functionality has been developed within ABACUS that allows for ‘single click’ exports of macrobenthic datasets that comply with internationally recognised data standards (e.g. MEDIN, GEMINI, ISO) facilitating rapid data ingestion with data archiving centres (e.g. DASSH). 

The system has also been developed with a ‘live link’ to key web resources including the World Register of Marine Species (WoRMS) ensuring use of the most up to date nomenclature. The long-term aim is to make ABACUS available to all UK laboratories undertaking similar analysis and potentially to laboratories, universities and other organisations globally.

 
Figure 8. The role of ABACUS in the flow of marine biological data (right)

UK GEMINI 2.3 is now live!  

The Association for Geographic Information (AGI) is pleased to announce publication of the latest release of UK GEMINI, the UK profile and guidance for producing metadata describing geographic information datasets, series, and services. If you are a data publisher, you need to use UK GEMINI in order for your metadata to work with the UK implementation of INSPIRE, via SDIs in the devolved administrations or directly to data.gov.uk. If you are a data user, you can use the search facilities in various portals to discover useful datasets. There is a European portal, a national UK portal (data.gov.uk), sub-national portals and domain specific portals. Some of these support machine-to-machine searching direct from your desktop GIS.

This new version (2.3) consolidates material previously spread across several documents - we hope you will find that makes it easier to create and understand the metadata records.

AGI is grateful to Defra for funding part of this work, and to various member organisations for allowing their staff to work on it, and to our web support company (Web Foundry). Members from BODC, BGS, EDINA, HS2, MEDIN, Office for National Statistics, and Ordnance Survey, and several individual members all contributed to the revision.

GEMINI lives at https://agi.org.uk/gemini 

News

MEDIN Business Plan 2019-2024 

The Marine Environmental Data and Information Network (MEDIN) are in the process of writing a new Strategy and Business Plan for the next 5 years. If you would like to propose areas that MEDIN should focus on in coming years, please contact MEDIN Co-ordinator, Clare Postlethwaite by 27th July 2018.    

Events

iPres 2022 comes to Glasgow! 

The Digital Preservation Coalition (DPC) will host the International Conference on Digital Preservation (iPres) in Glasgow in 2022.

The iPres conference is a global forum for research and development in digital preservation.  Held every year since 2004 it has been held on four continents, embracing a variety of topics in digital preservation from strategy to implementation, and from international and local initiatives.

 It welcomes small organizations and large; established leaders and new entrants. Year on year the debate and research profiled at iPres have moved digital preservation from a niche specialism of experts to a global challenge with the community to match.

 

'Beyond the Coast 2018' 

Last week, Gaynor Evans from the Marine Environmental Data and Information Network (MEDIN), was an invited facilitator at a conference on the future of our offshore marine environment. 'Beyond the coast 2018' was organised by the Joint Nature Conservation Committee (JNCC) and held at the University of Hull. The conference marked the 10th anniversary of the selection of the first set of UK Marine Protected Areas (MPAs).

The 2-day conference provided a great opportunity to hear about the status of the offshore environment from many expert stakeholders covering wide ranging subjects, including marine plastics, oil and gas licensing, ecosystem services and natural capital, fisheries, autonomous vehicles and eDNA.  Data management was front stage on the second day during one of the breakout sessions, when the work that MEDIN does was discussed in the context of the offshore environment. JNCC will be capturing the outputs from the conference with a special issue of conference proceedings in the Journal of Aquatic Conservation.   

Marine and Coastal Civil Engineering Expo, Birmingham 2018

More than 2,500 marine and coastal civil engineers will flock to Birmingham's NEC on 12 & 13 September, 2018.
 
Playing host to 150 suppliers, 100 expert-led seminars and 2,500 leading professionals from across the industry; the Marine & Coastal Civil Engineering Expo is home to the innovative infrastructural solutions and engineering concepts shaping the sector’s future.
 
And your free ticket also gives you access to the Contamination Expo Series, Flood Expo, RWM and Future Resource Expo - combining to create the world’s most influential environmental package.
 
Visit the M&CCE Expo website for your FREE tickets, or contact
Steven Bell on 01872 218 007 or steven.bell@prysmgroup.co.uk to enquire about the exhibiting and sponsorship opportunities.

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