- Work Packages
- WP 1Management & Coordination
- WP 2 (OSD)Ocean Sampling Day
- WP 3Oceanography & Environmental Data
- WP 4Standards and Interoperability
- WP 5Bioinformatics & Data Integration
- WP 6Exploring Ecosystems Biology
- WP 7Function and Biotechnology
- WP 8Intellectual Property (IP) Management for Marine Bioprospecting
- WP 9Dissemination & Outreach
- Public DeliverablesAll Micro B3's public deliverables
- Third Micro B3 Industry Expert Workshop
- Micro B3 Industry Expert Workshop
- Micro B3/OSD Analysis Workshop
- Micro B3 Stakeholder Workshop
- Micro B3 Summer School in Crete 2014
- Marine Metagenomics Bioinformatics
- Micro B3 Industry expert workshop
- EU-US Training 2013
- Micro B3 Statistics Training 2013
- MG4U Bioinformatics Training 2013
- Bioinformatics Training 2012
- EU-US Training 2012
Oceanography & Environmental Data
Rationale and objectives
The objectives of work package 3 (WP 3) are
- to establish interoperability between Micro B3 and the leading oceanographic environmental data management systems,
- to provide oceanographic environmental data to the project and
- to support management and curation of environmental and ocean data by providing data management skills.
By establishing interoperability, rich data sources of geo-referenced marine environmental biological and oceanographic data, expertise and data products are being made easily available for Micro B3 in an automated way.
The tasks in WP 3 are dedicated at establishing
- ''horizontal" interoperability with the genomic data infrastructure, as operated by ENA at EMBL-EBI, and
- "vertical" interoperability with the bioinformatics analysis system Micro B3-IS, developed in WP 5.
Work done in WP 3 is also providing input for the standards and interoperability WP 4. It will compile and deliver specific data sets and data products from existing data sources that are ‘fit for use’ for ecological analyses in WP 6. Additional data will be collected in the framework of Micro B3 via the Ocean Sampling Day (OSD, WP 2) and derived from the Tara Oceans expedition for which the WP 3 team will give data management support. Finally, the team will ensure that these newly acquired data sets are well processed and managed for use in the Micro B3 analyses.
WP 3 in cooperation with WP 4 and WP 5 established an agreed model for the data flow from the field (marine expeditions, monitoring stations) via data centres (National Oceanographic Data Centres, ICES, PANGAEA) to the European overarching data infrastructures for marine environmental data (SeaDataNet), for marine biodiversity data (EurOBIS), and for genomic data (ENA at EMBL-EBI). Moreover, a model for organising the data flows for sharing metadata and giving access to related data is established between these three European infrastructures. This includes but is not limited to how data are made available and feed into the Micro B3 Information System (Micro B3-IS). This is a major achievement, which will guide the further implementation and operation in the coming project period. It is expected to have a long-term effect paving the way to providing a common access for users to marine data from the diverse domains and infrastructures.
Long-term stations studied by Micro B3 partners useful as pilot sites due to good environmental data coverage are shown in the insert. Data hot spots from crossing data from environmental data providers with expedition data of both TaraOceans and Malaspina cruises are indicated by the boxes in the large graph.
Deliverable D3.1, which did a "Review of oceanographic data services for Micro B3", gives a description of the leading existing oceanographic data management infrastructures in Europe. They will provide to Micro B3 oceanographic and marine environmental data from existing data collection activities from multiple sources. The review describes in detail the set up, scope and services of SeaDataNet, including its network of connected data centres, as well as of EurOBIS, and their roles in the EMODnet development.
New data will be derived from the Tara Oceans expedition for which WP 3 will give data management support via partner UniHB using PANGAEA. This is specified in Deliverable D3.2 ''Plan for supporting data management for Tara Oceans cruise".
Deliverable D3.3 "Analysis and definition of interoperability of oceanographic services with Micro B3" was produced by WP3 in coordination with WP 4 and WP 5. It gives a functional analysis of the way that the flow of data from the field via the data management infrastructures to the Micro B3-IS and its users might be structured and organised. Furthermore D3.3 gives a technical analysis and specifications of the interoperability options, both for delivering metadata and data to Micro B3-IS and for the mutual exchanges between SeaDataNet (marine environmental data), EurOBIS (marine biodiversity data) and the European Nucleotide Archive (ENA for molecular sequence data).
Recently, WP 3 published Deliverable 3.4 "Selection and definition of geographical pilot areas for Micro B3 cases", which defines the locations, which were selected as matching areas with Micro B3 genomic and oceanographic data relevant for the Micro B3 Use Cases. The portal and the services gathering and delivering environmental data in the Micro B3-IS structure (i.e the interfacing between SeaDataNet-EMODNet services and the Micro B3-IS) are planned to be shown to work for specific geographical sites. Further detailing and actual implementation of the interoperability solutions, followed by the operational provision of oceanographic data to Micro B3, will take place in the second and third year of the Micro B3 project.
Lead of WP 3: Dick Schaap, Marine Information Service