Today's mission: glider data management

Three members of the British Oceanographic Data Centre (BODC), Justin Buck, Mark Hebden and Lise Quesnel, have just returned from a scientific mission where they worked with colleagues to formalise protocols for glider data management across Europe.

A Slocum glider starting its mission. ©

Gliders provide a relatively low cost method for acquiring data remotely. They perform missions to traverse oceanographic areas of interest collecting data as they go. In recent years, the technology has matured sufficiently to make these platforms a very effective means of data collection. Therefore it is important that glider missions be supported by an appropriate data management strategy, ensuring that data and metadata are preserved in a sustainable format that is exchangeable between communities.

As the nominated Data Assembly Centre (DAC) for UK glider data, BODC joined colleagues from the Centre for Maritime Research and Experimentation (CMRE) in Italy and the host organisation, Ifremer, for the week long mission in Brest. The goal was to create consistent and coordinated European glider data management procedures. Funding came from the EU FP7 Gliders for Research, Ocean Observation & Management (GROOM) project, under the Everyone's Gliding Observatories (EGO) initiative.

Over the course of the week guidelines were finalised, real-time quality control procedures were developed and a preliminary 'EGO format' for glider data (based on SeaDataNet Climate and Forecasting (CF) compliant NetCDF) was generated.

BODC are committed to ensuring that UK glider data are managed in a way that will ensure their long-term value. Achieving full interoperability with the international community will help to achieve that goal. Routine channelling of the UK's near-real-time glider data to a Global Data Assembly Centre (GDAC) for Europe will begin in 2013.

Nations united by a common language

The quote "Two nations separated by a common language", attributed to George Bernard Shaw, has often been used to describe the relationship between the UK and the USA. On Friday 7th December 2012, however, at the Fall Meeting of the American Geophysical Union in San Francisco, it appears that, in the words of Bob Dylan, "the times they are a-changin'".

Adam Leadbetter attended the meeting and presented a poster on the BODC's web services for the NERC Vocabulary Server version 2.0 (NVS2.0) in the session "Semantics and Cyberinfrastructures for Next Generation Science".

George Bernard Shaw, 1936. Image courtesy of Wikimedia Commons ©

The NVS2.0, developed by the British Oceanographic Data Centre (BODC) over recent years with funding from NERC and the EU NETMAR project, provides access to controlled vocabularies and is used by the wider environmental science community. Within NETMAR, NVS2.0 has been used or

• semantic validation of inputs to chained Open Geospatial Consortium (OGC) Web Processing Services
• smart discovery of data and services
• support for multiple human languages
• integration of data from distributed nodes of the International Coastal Atlas Network (ICAN)

Since its deployment, NVS2.0 has been adopted within the European SeaDataNet community’s software products.

Crossing the Atlantic

Meanwhile, at the meeting in the "Linked Data for Earth and Space Science" session there were three posters, presented by colleagues from the United States, showing their use of the BODC NVS2.0 web services.

• Adam Shepherd and Elizabeth Coburn from Woods Hole Oceanographic Institution (WHOI) demonstrated both a Drupal-based website that allows mappings to terms in our vocabularies and a shipboard event logging system, which uses those same vocabularies
• Robert Arko from Lamont-Doherty Earth Observatory (LDEO) showed how the Rolling Deck to Repository (R2R) project links data from US university research vessels to other repositories using concepts from the NERC Vocabulary Server

Poster references

The NERC Vocabulary Server: Version 2.0. Adam Leadbetter and Roy Lowry.

Maintaining Scientific Community Vocabularies in Drupal through Consumption of Linked Open Data and Web Services. Adam Shepherd et al.

Controlled Vocabularies and Ontologies for Oceanographic Data: The R2R Eventlogger Project. Elizabeth Coburn et al.

Rolling Deck to Repository (R2R): Linking and Integrating Data for Oceanographic Research (Invited). Robert Arko et al.

All presented at:
American Geophysical Union
San Francisco, United States. 03 - 07 December 2012.

Today's recipe: how to build a bathymetric grid

The General Bathymetric Chart of the Oceans (GEBCO) community aims to provide the most authoritative publicly available bathymetric data sets for the world's oceans.

In order to assist and encourage further participation in bathymetric grid development work, GEBCO has created a technical reference manual, the IHO-IOC GEBCO Cook Book, on how to build bathymetric grids.

Download a copy of the IHO-IOC GEBCO Cook Book  (14.3 MB).

The IHO-IOC GEBCO Cook Book. ©

The Cook Book recipes

The Cook Book includes input from a number of individuals and organisations, all of whom are experts in their respective fields. It is aimed to update and extend it with new contributions as they become available. It includes a wide range of topics, for example

• gathering data
• data cleaning
• gridding examples
• software overviews

The Cook Book is maintained and made available by the Chairperson of the GEBCO Cook Book Working Group, Dr Karen Marks, at the US National Oceanic and Atmospheric Administration (NOAA) Laboratory for Satellite Altimetry.

Reference

The IHO-IOC GEBCO Cook Book (2012). IHO publication B-11, IOC Manuals and Guides 63, 221pp.

On behalf of the project, GEBCO’s bathymetric grids are maintained and made available by the British Oceanographic Data Centre (BODC).

One million Argo profiles

Argo, an international project initiated in 2000, aimed to establish a global network of profiling floats. It achieved its first goal of 3000 operating floats in October 2007 and on 30th October 2012 met another milestone — one million data profiles.

The millionth profile arrived at the Global Data Assembly Centres (GDAC) on 31/10/2012 at 16:50:07. This profile was transmitted by NOAA-PMEL float 5901891, cycle 146.

The Argo folding globe ©

Each year around 800 floats need to be deployed to maintain the 3000-float array This array provides around 100,000 observations per year and floats operate throughout all the ice-free deep-ocean areas of the world.

The British Oceanographic Data Centre (BODC) is a national-level data centre in the Argo data processing chain hosting floats from the UK, Ireland, Mauritius and Saudi Arabia. This represents approximately 4% of the array.

We have updated the folding globe to celebrate the one million profiles — the updated version indicates the current status of the array.

Numerical model data portal

In line with our commitment to improve data access, the British Oceanographic Data Centre (BODC) announce the launch of our numerical model data portal. This provides searching, visualisation and data download mechanisms for numerical model data.

Initially the portal is populated with output from the Coastal Flooding by Extreme Events (CoFEE) project. As the data from more models become available they will be added to this portal.

An illustration of the visualisation service ©

Numerical models

Numerical models are mathematical simulations of environmental processes based on understandings gained from direct observations and/or theoretical analysis. They help scientists and managers to predict, understand and adapt to changes that may affect people and their environment.

More about the portal

The main features of the portal are

• An easy to use, anonymous interactive search — search for data prior to registration or log in. Search options include geographic area, date, data parameter, model and simulation.
• A visualisation service — this includes animations, cross-section plots and more. This functionality requires user registration and log in.
• 'Online shopping' — add model data to a basket and check out your request.
• File generation — Climate and Forecast (CF) netCDF files are prepared by subsetting on user criteria using OPenDAP technology. For large volume requests or during busy periods data preparation may take a while. The file generator service emails the user when the data are ready for download.
• Request tracking and download service — 'my account' services allow users to track their request and return to download data at their convenience.

Acknowledgements

Special thanks are due to Jon Blower at the Reading e-Science Centre (ReSC) who kindly gave us his permission to incorporate his visualistion software as part of our numerical model data portal. We are also grateful to the British Atmospheric Data Centre (BADC) for their advice on aspects of this development.

Adding 'sparkle' to the NERC Vocabulary Server

The British Oceanographic Data Centre (BODC) announce the launch of a SPARQL Protocol and RDF Query Language (pronounced 'sparkle') end-point for the NERC Vocabulary Server (NVS2.0). This new service allows the retrieval and manipulation of data stored in Resource Description Framework (RDF) triples.

Sparkling seas ©

Previously, the only access to the vocabularies stored in NVS2.0 had been through a custom interface. The SPARQL end-point has the following advantages

• It makes collections (vocabularies) appear as databases and gives the user powerful query mechanisms
• It enables users to interrogate multiple collections (that include SPARQL end-point functionality) with one customised query
• Queries are unambiguous as they must conform to a World Wide Web Commission (W3C) standard
• Results can be returned in a variety of formats. For example: Extensible Markup Language (XML), JavaScript Object Notation (JSON) or Comma-Separated Values (CSV)

What are RDF triples?

Imagine a simple vocabulary that describes flower colour. Its contents could include: 'A buttercup has the colour yellow', A daffodil has the colour yellow', 'A tulip has the colour yellow','A tulip has the colour red', 'A tulip has the colour orange', 'A tulip has the colour pink'.

Where 'A buttercup has the colour yellow' in RDF is the triple; 'A buttercup', 'has the colour', 'yellow'.

Using SPARQL, you could easily identify those flowers that have the colour yellow or all the tulip colours. This could be federated to collate information from any 'flower colour' vocabulary with a SPARQL end-point.

The NERC Vocabulary Server

To ensure consistent metadata and data descriptions, the NERC Vocabulary Server (NVS2.0) provides access to the controlled vocabularies used by both BODC and the wider environmental science community. The vocabulary concepts are linked by mappings to provide RDF triples.

Gliding over the edge

Mark Hebden, a British Oceanogarphic Data Centre (BODC) Data Scientist, recently returned from RRS Discovery cruise D376. This is the first cruise for Fluxes Across Sloping Topography of the North East Atlantic (FASTNEt). FASTNEt is a four-year initiative that aims to improve our understanding of the physical and biogeochemical exchange taking place across continental shelf edge margins. From the start, BODC have been working with FASTNEt scientists to ensure the provision of adequate data management.

Following a successful mission the scientists onboard D376 recover their glider. ©

Shelf edge regions mark the gateway between the world's deep oceans and its shallower coastal seas. They link terrestrial, atmospheric and oceanic carbon pools. Shelf margin processes have a direct influence on near-shore productivity (and consequently fisheries) as well as affecting global climate.

Traditionally, research cruises have offered a brief opportunity to collect data; we still have only snapshots of marine environments. D376 was notable for its ambitious data collection regime. The combination of traditional sampling techniques coupled with novel autonomous technologies represents a new era in observational oceanography.

D376 deployed four gliders at the shelf edge. Gliders are autonomous vehicles that use small changes in their buoyancy to descend and ascend through the water column. Three of these gliders will be gathering data on and off the Celtic Sea shelf until autumn 2012. Between dives, scientific sensors will collect near-real-time data and transmit them via satellite back to shore.

Data Scientist cruise participation strengthens project relationships and increases familiarity with data streams. This has a direct influence on the efficiency of data assimilation to the data centre. While at sea, Mark was responsible for compiling accurate and complete metadata — essential information about data.

The cruise also marked another significant milestone, one which nods firmly to the past. With the scientific objectives completed, RRS Discovery set sail for port, arriving on the eve of the 50th anniversary of her launch. Discovery will be taken out of service later this year. Her replacement will take over in 2013.

Discovery has played a central role in marine research, from charting the ocean floor, contributing to climate change research and discovering marine species. An important and significant legacy of data, for use long into the future, remains as a fitting testament to 50 years of research.

NERC Vocabulary Server

The British Oceanographic Data Centre (BODC) announce the launch of a new version of the NERC Vocabulary Server.

An example of the returned XML document ©

Version 2.0 (NVS2.0) of the server represents a complete rewrite of the internal software, with increases in both functionality and performance. The information returned from calls to the Vocabulary Server has also been redesigned and enhanced to take in to account the latest available standards. Other enhancements include the ability to provide information in multiple languages and for links to be made between the content of the NERC Vocabulary Server and other resources.

Although the code for version 1.1 (V1.1) will remain operational for the foreseeable future, existing users are urged to convert to NVS2.0 as soon as possible. The development of new applications based on V1.1 is strongly discouraged.

NVS2.0 has been developed as part of the European Union Framework Programme 7 funded Open Service Network for Marine Environmental Data (NETMAR) project.

Published Data Library (PDL)

The British Oceanographic data Centre (BODC) announce the launch of an operational prototype Published Data Library. This provides snapshots of specially chosen data sets, archived using rigorous version management. This enables citation of the data set in journal papers through the assignment of a Digital Object Identifier (DOI) in collaboration with the British Library.

An example of a dataset citation. ©

The PDL is for the publication of fixed copies of reference data sets so that they can be re-used and cited over an indefinite period of time. There is a fundamental assumption that the copy of the data set will be exactly the same each time it is referenced. It should be noted that the assignment of a DOI is not a substitute for long-term data management by the NERC data centres, which enables users to construct their own data sets from all data holdings.

Consequently PDL data sets will be restricted to two types

1. Data sets that have not yet been ingested into the BODC system, but are destined for future ingestion.
   Candidate data sets will be identified through discussion between data originators and the BODC data scientists responsible for the data. The data originator has full responsibility for providing data and metadata that meet the technical quality standards. BODC will judge the acceptability of data sets in terms of their completeness, but not in terms of their scientific quality or value.
2. Data sets that have been ingested into the BODC system and subsequently exported.
   Candidate data sets of this type will be identified through discussion between the scientists who supplied the data and the BODC data scientists responsible for their ingestion. The technical quality of these data sets is BODC's responsibility.

Data citation is an exciting and rapidly evolving area of science publication and it is likely that the approach will take time to mature. While we aim to provide an efficient service, a heavy takeup for publication will inevitably take time to process. To help everyone, we would be grateful if contributors to the PDL plan well ahead, contact us early and take time to become familiar with the necessary requirements for submission.

Work is continuing in this area as BODC are committed to improving the services we provide to the marine community.

Data management for the UKOA programme

The British Oceanographic Data Centre (BODC) announces the launch of the data management area for the UK Ocean Acidification (UKOA) research programme.

Chalk cliffs today are the legacy of carbonate shells produced by marine organisms in the distant past ©

UKOA is a five-year, £12 million research programme that began in 2010. It involves 27 research institutes in the UK, has close links with other ocean acidification programmes around the world and is co-funded by the Natural Environment Research Council (NERC), the Department for Environment, Food and Rural Affairs (Defra) and the Department of Energy and Climate Change (DECC).

Ocean acidification occurs as carbon dioxide (CO₂) dissolves in seawater and forms carbonic acid. The oceans absorb roughly half of human CO₂ emissions and, if we continue emitting CO₂ at the same rate, the acidity (hydrogen ion concentration) of the upper ocean is predicted to increase by about 150% by 2100. This pH change has other important implications for ocean chemistry – and marine life.

UKOA aims to better predict the chemical changes involved and their knock-on effects for organisms and ecosystems and thereby help provide effective policy advice on the potential size and timescale of risks.

BODC's role involves the quality control, dissemination and stewardship of UKOA data, as well as facilitating data exchange within the UKOA community and providing advice on data management best practice. Our data management web pages provide background information about the UKOA programme, as well as inventories of research cruises and associated datasets.
The pages are designed to promote data sharing and collaboration between programme participants and the wider scientific community.

BODC at Oceanology International 2012 (Oi2012)

The British Oceanographic Data Centre (BODC) are participating in Oceanology International 2012 (Oi12). It takes place from 13-15 March 2012 at ExCeL London, the international exhibition and conference centre in the Docklands.

BODC stand at Oi10. ©

Oceanology International is a global forum where industry, academia and government share knowledge and connect with the marine technology and ocean science community, looking to improve their strategies for measuring, exploiting, protecting and operating in the world's oceans.

A huge selection of marine technology suppliers will be exhibiting their latest innovations and the event will also include a conference, visiting vessels and live demonstrations. There will also be a Careers Day, which should provide good opportunities for student outreach.

As ever, BODC will have our own stand (it's L250 if you're looking for us) and we'll be demonstrating our current projects and developments. Here's the floorplan of the stands at Oi12, so come and visit us and pick up a BODC brochure, a free General Bathymetric Chart of the Oceans (GEBCO) poster (showing the GEBCO world map) and a BODC badge!