Marine Biodiversity and Ecosystem Functioning
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[ Overview ] [ Objectives ] [ Spreading Of Excellence ] [ Partners ] [ Associated Partners ] [ Committees ]
[ Project Management ] [ Data Management ] [ Taxonomic Clearing System ] [ Quality Assurance ] [ Training ] [ Outreach ] [ SMEs ]
[ Theme 1 Global Patterns ] [ Theme 2 Ecosystem Functioning ] [ Theme 3 Socio-economics ]

Data Management

Data Systems Website

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Promote communication and integrative data management

MarBEF will espouse the philosophy of data sharing. Access to very large scale data sets will bring unique benefits, the most important of which is that such data sets can reveal patterns not apparent in small scale data. The IT heart of MarBEF will be a specialised search engine and a series of interlinked databases, including several existing databases, such as ERMS. They will allow network members to know what research is being done, or is planned, throughout the network and it will enable them to better plan and integrate future research. The core facility will be a distributed database containing information about all of the marine species known to occur in European waters, with details of sites from which they have been recorded. The biological data and associated physical data will form the basis for ongoing research into marine biodiversity research across Europe, ranging from long-term, large-scale studies to small-scale, short-term investigations. This system will be designed for sharing data: only by pooling our data resources across Europe can we become truly competitive when addressing the big questions in marine biodiversity and ecosystem science. The MarBEF portal will be linked to existing regional and global databases, such as GBIF, ERMS, ASFA, FishBase, AlgaeBase, OBIS (Ocean Biogeographic Information System), British Oceanographic Data Centre (BODC), SAHFOS and MBA-MarLin, all of which have invaluable expertise as well as data relevant to our objectives.

Developing an integrated data and information management system

Information on the existence of data is a prerequisite to data sharing. MarBEF will inventory all aspects of marine science relevant to marine biodiversity; in this collaboration will be sought with existing initiatives such as MEDI and EDMED. A database will be created storing information on planned, ongoing and finalised research. Lists of institutions, scientists and their expertise and publications will be maintained. A database of research facilities, oceanographic vessels and cruises will allow efficient sharing of resources. The most important type of information will consist of an inventory of existing biodiversity databases. These will be documented, giving details on taxonomic scope, information content, access constraints and quality, and where possible a direct link provided to an internet entry to the data.

A second step covers the need to create massive data sets on species and biogeography. MarBEF will establish a public European warehouse of biological databases together with intelligent tools for data mining. Development will be undertaken so that marine biological data sets will be accessed at their host institutes by the central MarBEF portal to build maps showing distribution of species and biotopes. The inventory of biodiversity data sets will be instrumental in identifying candidate data sets for integration. The work will be undertaken with and take advantage of development already undertaken by the Ocean Biodiversity Information System (OBIS) so that a facility will be developed known as EurOBIS. To facilitate exchange of research results, data formats and standards will be proposed; in this, efforts of other groups will be re-utilised. Links will be established with TDWG, ICES/MDM, IODE/GE-TADE, IODE/GE-BCDMEP and others for data standards for biological data. The taxonomic backbone to all the data activities will be the European Register of Marine Species. Mechanisms will be developed to keep the ERMS up-to-date, and synchronous with major data contributors such as ETI's World Biodiversity database, FishBase, Algaebase, CLEMAM and many others. ERMS will be available as a fully searchable database though two or more web sites. The use of a central register of taxonomic names will improve the quality of integration of data from several sources. MarBEF will represent its members in international activities on data management, such as IOC, OBIS and GBIF; based on its accumulated data and tools, it will be able to play a leading role in such initiatives.

Data Integration

Objectives
  • To provide visibility to the network by creating a web site, including information on the network, its partners and their activities and research results
  • To facilitate an unhampered and free exchange of data between partners within the network and to enhance the integration of information
  • To promote the interoperability of data sources of the network with other relevant information sources by the development of appropriate tools, standards, and protocols
  • To promote utilisation of the data by providing added value to existing data
  • To enable a common European approach to future data management and storage by the use of a common suit of tools
  • Liaise with OBIS, ENBI, GBIF and Species2000 for alignments of philosophy and IT approaches

Description of work

Task 1: Establish MarBEF web site
A dedicated network website will be developed, with a suitably high profile domain name (e.g. www.marbef.org or www.embef.org). The site will be multi-lingual in part with three main sections:

  • Management section (management activities), including:
    • general management and project information
    • description of the network, including list of participants and link to institutions
    • details of themes and structure of the network
    • summary project activities and results
    • documentation on network best practices (see Quality Assurance activities)
  • Data management and integration section (integrating activities). This section will contain several main sub-databases:
    • Information database (see task 2)
    • Metadata database (see task 3)
    • Taxonomy database (see task 4)
    • Biogeography data portal (see task 5)
  • Outreach section (see Spreading of excellence activities)
The information now available on the BIOMARE site will be incorporated in the MarBEF site. The website will be hosted at a single location, but several sections will be maintained from remoter locations (e.g. the outreach section will be maintained and updated from EcoServe. Access to certain databases will be on the basis of passwords; sections of the web site will only be accessible to network members; other sections will only be accessible to partners in specific projects.

Task 2: Develop information database: web-based register of resources
A central database holding resource data will be established. Information will be gathered from existing sources and updated. New sources are targeted through expertise in the network. Data will include:

  • People/expertise
  • link with EDMED, IODE: GLODir, ERMS, etc
  • Organisations
  • link with EDMED, IODE: GLODir, BIOMARE, ERMS, MARS
  • Literature: first phase publications by network members, branded as MarBEF/EMBEF publications; later possibly all publications relevant to marine biodiversity that are known to network members
  • also grey literature: research reports… These usually contain more detailed results than peerreviewed articles in major journals. Also, articles in major journals are easily traceable through international, commercial abstracting services.
  • need to keep track of institutional affiliation of individual authors
  • Projects, including
  • 'Expression of interest'
  • also activities that are not strictly 'formal', separately funded projects
  • link with EDMERP
  • Events (conference, workshop…)
  • Datasets
  • link with IOC/IODE (MEDI),
  • link with NASA: Global Change Master Directory
  • link with EDIOS
  • Sampling gear/equipment/research platforms
The central database will allow scientists and institutes to remotely create and maintain their own record. Formats and protocols to upload larger volumes of data e.g. XML, to link with IODE and ICES activities will be developed. All resource data will be described using standard vocabulary using e.g. ASFA thesaurus terms for keywords; ITIS and/or ERMS names for taxonomic names; IHO and/or ASFA (and others?) for geography. Existing efforts to integrate data under the umbrella of the EU, e.g. EuroCRIS/CERIF will be studied and incorporated into the scheme. The database of people and organisations will also serve as a register of contacts for outreach. The structure of the database will allow querying these contacts separately. Ecoserve will be responsible for input for these contacts.

Task 3: Develop metadata database
A key task in integrating resources is to identify what resources are currently available answering the questions who has done and who it doing what? Such an inventory will be made available via a searchable web site. The resource data will not be restricted to biodiversity information but also to oceanographic datasets and include information from:

  • Sites e.g. BIOMARE, Natura 2000, etc
  • Surveys/cruises/sampling campaigns
  • List of past and planned cruises; planned cruises are instrumental if we want to encourage scientists to join cruises in other institutions
  • Linking with ICES cruise summary report database and other existing schemes such as the Canadian - 'National oceanographic plan'.
  • Samples
A set of distributed databases; needs agreements on structure and protocols for exchange, and integrating interface on portal

Task 4: Develop a distributed marine taxonomic register
Common access to an array of interoperable distributed databases holding information on species of relevance to European biodiversity research will be established. The array of databases will be queriable through a single search engine on a common web access point. The thus formed virtual taxonomy register is a key element to promote the proper use of taxonomic names, and thus scientific communication, across the network.

A main building block will be the ERMS; other important building blocks include URMO (UNESCO Register of Marine Organisms), and ETI's North Sea Information System. Scientists who developed species lists in these databases will be contacted and asked for a revision of the taxonomic lists. Additional information such as taxonomic hierarchies will be stabilised and synonyms and other information added. Existing OBIS tools and techniques for management and analysis of biodiversity data will be applied to European data. ETI, leader of ENBI's cluster III 'Common access and Interoperability' will provide the link with both ENBI and GBIF for data standards and IT approaches and will ensure that the MarBEF network will be globally visible.

HMSC is leading the development of the North Atlantic Register of Marine Species (NARMS). This will expand and update the European Register of Marine Species (ERMS), a MAST project that compiled the first checklist of marine species for European Seas. HMSC also hosts the OBIS secretariat. HMSC has completed electronic lists of marine life for the Bay of Fundy and is collaborating with other Canadian and USA scientists to expand these lists. It has applied for funds to combine ERMS and these lists to produce NARMS; funding is requested from MarBEF to update and address gaps in ERMS, including funds to subcontract taxonomic experts, host workshops, and coordinate this initiative. European synergy on data formats, standards, database structure, and protocols for data exchange, taxonomic unison and approriate IT tools will be established in consultation with:

  • OBIS, ETI, TDWG, ICES MDM, IODE GE/BCDMEP for structures and protocols
  • ERMS, FishBase, Algaebase, the UNESCO Register of Marine Organisms, ITIS, ETI, Species 2000 for taxonomic information
  • OBIS and ETI for IT tools
Task 5: Develop portal for distributed databases
MarBEF will not try to establish a large central database but instead focuses on using approaches such as developed by e.g. OBIS, ENBI and GBIF to support queries to an array of dispersed databases, leaving the maintenance and update in the hands of their owners and developers. To enable this process, common formats, standards and procedures will be developed; whenever possible, existing formats, standards and procedures will be used. This exercise will be conducted in collaboration with the network of organisations with technical expertise in biological data exchange developed under task 4.

GBIF and the Biodiversity Information Standards (TDWG), are developing data standards, protocols, reviewing existing datasets, IPR agreements, and compiling central taxon dictionaries (through initiatives like EDIT, EoL, CoL and PESI). While TDWG is, in principle, an initiative that covers both terrestrial and marine biodiversity, there is a strong emphasis on terrestrial and botanical systems. MarBEF will work together with TDWG, GBIF, PESI and Species2000 to provide marine biodiversity input, and complement the their databases.

The MarBEF portal will be the European node to OBIS. Through collaboration with OBIS the scientific community will have rapid free access to data on marine species distributions, and ocean environmental data and 'climate' (extrapolated or mapped statistics on average sea surface temperature for example). In addition, OBIS provides, and is developing more, on-line tools for data handling, mapping and analysis. These tools will be available to MarBEF, as well as the experience, advice, and data accessed by OBIS. Through OBIS European scientists will be able to study patterns across the North Atlantic for example, or compare spatial and temporal patterns between east and west Atlantic. For example, differences in biodiversity between the Gulf of Maine and North Sea benthos or fish stocks may be compared to ocean climate conditions.

Task 6: Data Management Workshop
A data management meeting will be organised soon after the official start of the network: 'Data management in MarBEF: principles and practices'. During this meeting, data exchange policy will be discussed, and priorities for integrated databases and further data management activities. These priority activities will then be, together with the network partners, turned into new Work Packages. Representatives of relevant research and development programmes (GBIF), networks (ENBI), projects (Species2000) will be invited to ensure broad international input and a alignment of European standards, protocols adopted by MarBEF.

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