Existing networks

The European Biodiversity Portal (EBP) is not aiming to upload any data by itself. Insteed, it will draw on already existing registries/catalogues and will integrate them with the GEOSS Common Infrastructure (GCI). Several specific components and sub-networks have already been identified for integration in EU BON. In addition to GBIF, these include, e.g., the broader DataONE network (including LTER, KNB, ILTER, Dryad), DaEuMon and DEIMS. For uploading data and metadata, catalogue or repository a software will be installed on each testing site or data provider, e.g. DEIMS, Morpho and MetaCat.The system will be able to search biodiversity data and metadata from a wide range of data providers. During the first phase of the development, the system will integrate the following data providers:

 

 

GEO BON (Group on Earth Observations Biodiversity Observation Network) is a network of networks for understanding biodiversity change on earth (Scholes et al. 2012). Its vision is: coordinated, global network that gathers and shares information on biodiversity, provides tools for data integration and analysis, and contributes to improving environmental management and human well-being. The information components of GEO BON have been outlined in the GEO BON Detailed Implementation Plan and its associated technical document (Ó Tuama et al. 2010). GEO BON draws on GEO’s work on data-sharing principles to promote full and open exchange of data, and on the GEOSS Common Infrastructure to enable interoperability through adoption of consistent standards.

GEOSS

The Global Earth Observation System of Systems (GEOSS) is an initiative lead by the Group on Earth Observations (GEO) to link together already existing observation systems in the service of several “Societal Benefit Areas” including biodiversity and ecosystems.

The GEOSS Common Infrastructure (GCI) allows the user of Earth observations to access, search and use the data, information, tools and services available through the Global Earth Observation System of Systems.

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LifeWatch (e-Science infrastructure for biodiversity and ecosystem research) is a research infrastructure proposed by the European Strategy Forum on Research Infrastructures (ESFRI). LifeWatch itself is not an infrastructure generating data, but an environment, mainly for the biodiversity community, for discovering, processing, modelling and collaborating on data (including software tools).

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The Global Biodiversity Information Facility (GBIF) is a major integrator of biodiversity occurrence data and thus a top priority for integration in EU BON. The GBIF informatics architecture provides unified access via a web portal and web services to a global network of data publishers. Through appropriate standards and tools, the infrastructure is designed to serve three main types of data: metadata (i.e., descriptions of datasets), primary biodiversity data and names data. These data are made available online by numerous GBIF Nodes for central harvesting by GBIF which indexes and integrates the content and makes it available for discovery, retrieval (e.g., via web services) and analysis.

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LTER-Europe (European Long-Term Ecosystem Research Network) is an essential component of world-wide efforts to better understand ecosystems. LTER-Europe consists of both the main LTER web site and national LTER networks. LTER aims to integrate data and databases through an ontology covering any kind of object and its parameters in the field of LTER research. The Drupal Ecological Information System (DEIMS) was developed as a portal for sharing metadata within the LTER network. In DEIMS, end users can describe, discover, view and download information about data sets, research and observation websites, bibliographic references and personnel information. Metadata associated with data sets is modelled using EML and, of particular interest, a form-based tool is provided in DEIMS for uploading data sets and easily generating associated metadata in EML.

Find more information on DEIMS and GeoNetwork in Tools repository

 

Interoperability and data integration with the DataOne network has been prioritised in the EU BON project. The architecture of DataONE network needs therefore to be reviewed in order to ensure compatibility. DataONE is a distributed network of repositories (Member Nodes) and currently four search facilities (Coordinating Nodes), which contain resource descriptions of the Member Nodes.

The Member Nodes maintain a preservation-oriented repository. Different repository products may take different approaches to data preservation, but in general they

  • use persistent identifiers for data products
  • ensure access to these data products over the long term
  • ensure that metadata documents exist alongside the data products

A data package in DataONE uses Metacat (see Tools) as its data sharing platform. However, to make data integration possible, the EU BON platform would not support just any kind of data to be shared. The data would need to comply with standards like EML, ABCD or Darwin Core with its new extensions for ecological measurement
data. This would allow Metacat to be used in similar ways to the GBIF data provider tools. The portal would be able to download raw data tables from Metacat providers and index the data.

See Screencast tutorials how to use DataOne tool.

 

The DaEuMon database provides information on biodiversity monitoring in Europe, national responsibilities, and biodiversity coverage of the Natura 2000 network. Policy briefs for these topics are also available. It also provides a support tool called BioMAT for the design and analysis of monitoring schemes.

This database has been identified as a key resource for EU BON. It requires enhancement on two fronts: the coverage needs to be increased from the current 643 entries at least two-fold and the database model needs to be enhanced to cover issues of access interfaces, download of data, terms of use and database details.

he portal

 

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).  GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.

 

 EU Nomen enables the correct use of species names and their classification, to more accurately manage information on animals and plants. This is the first all-taxa inventory for European species.

A Pan-European Species directories Infrastructure (PESI) is the next step in integrating and securing taxonomically authoritative species name registers that underpin the management of biodiversity in Europe. PESI will integrate the three main all-taxon registers in Europe, namely the European Register of Marine Species, Fauna Europaea, and Euro+Med PlantBase in coordination with EU based nomenclators and the network of EU based Global Species Databases . It is a standards based, quality controlled, expert validated, open-access infrastructure for research, education, and data and resource management.