EU BON and CETAF joint informatics workshop

The 2nd EU BON training on data sharing tools has taken place side by side to CETAF/EU BON informatics workshops (see full program and presentations). The event was organised by UEF and Digitarium, EU BON consortium member and work package leader (WP2), in collaboration with CETAF ISTC and other EU BON work packages.


Next topics were covered:

  • Introduction to GEOSS, GEO BON, EU BON (Hannu Saarenmaa):

Presentation: GEOBON_GEOSS_infra-v5.pdf

The presentation will cover origins, organisation, and current plans of the Group on Earth Observation (GEO), the goals and information architecture of the Global Earth Observation System of Systems (GEOSS).  GEOSS Portal, registry system, data sharing principles, available data, and brokering mechanisms will be explained. Participation in the GEOSS Architecture Implementation pilot process will be discussed. The GEO Biodiversity Observation System (GEO BON) and its aims for information management will also be covered.

  • Information architecture of EU BON (Antonio Garcia):

Presentation: 2nd_Training_EU_BON_Architecture_v03.pdf

The presentation will cover the current update or the software architecture that will support the EU BON Biodiversity Portal, focusing on the brokering alternatives and data/metadata sharing standards (EML, OGC-CSW, SOAP and REST interfaces..). We will introduce GI-cat as a brokering tool to integrate new data sources. This session will also include a demonstration of the first implementation prototype of the EU BON Biodiversity Portal.

  • Data standards, Darwin Core and extensions for sample-based quantitative data (Éamonn Ó Tuama):

Presentation: DwC-sample-data-Joensuu-final.pdf

The Darwin Core vocabulary, extended with a small number of additional terms, can be used in a Darwin Core Archive to encode information from sample-based data sets, i.e., data sets associated with environmental, ecological, and natural resource investigations. Such data are usually quantitative, calibrated, and follow certain protocols so that changes and trends in populations can be detected. This session introduces the new terms, the star schema model underlying Darwin Core archives consisting of a core table linked to one or more extension tables, and the associated enhancements to the GBIF Integrated Publishing Toolkit (IPT) to support publishing of sample-based data.

  • Demonstration of GBIF/EU BON IPT for monitoring networks (Larissa Smirnova and Franck Theeten):

Presentation of Larissa Smirnova on EU BON IPT publishing: EU BON_Presentation_IPT tool.pdf

Presentation of Franck Theeten on vocabularies: eubon_vocabularies_only_Theeten.pdf

Presentation of Franck Theeten on EU BON IPT: eubon_ipt_only_Theeten.pdf

The Integrated Publishing Toolkit (IPT) is a software tool developed by GBIF, aiming to facilitate the sharing and publishing of biodiversity data on the Internet using the GBIF network. It uses the Darwin Core standard to map species occurrence datasets and checklists, and can also handle data from natural sciences collections or observations. Since additional, sample-based terms are added to the DwC vocabulary, the IPT tool can be used by various monitoring networks collecting mainly quantitative data (environmental, ecological, and natural resource investigations). The practical part of the training will present the IPT tool, and explain how to publish your dataset  using the IPT tool, via a practical example using occurrence data.  Extensions of the IPT will be presented and issues will be discussed after the training…

  • Practical exercise with sample dataset (Larissa Smirnova and Franck Theeten)

Presentation of Israel Peer on example of sample-based data: EventBaseExample-gluecad (1).pdf

  • Practical exercise with own data (all trainees)

The workshop included lectures (see presentations above) and hands-on work. You can read and learn how to install the IPT tool  and publish your data here.

Place and date: Joensuu, Finland, 19 March 2015

Venue: Joensuu Science Park, Digitarium and the Conference Facility “Network Oasis”




Event type: 




Joensuu Science Park, Länsikatu 15 (P.O. Box 111), FI-80101 Joensuu


Start date: 

Thursday, March 19, 2015 - 09:30

End date: 

Thursday, March 19, 2015 - 17:30