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Improving technical cooperation and interoperability at the e-infrastructure level
Pavel Stoev

There is an increasing demand for biodiversity data, information and knowledge by the public and stakeholders. For this information to be widely available the existing technical barriers for interaction of e-infrastructures have to be opened. The pro-iBiosphere project has been launched for a period of two years (September 1st, 2012 to August 31st, 2014), with the goal of addressing technical and semantic interoperability challenges and preparing the ground for the creation of a system for intelligent management of biodiversity knowledge which will improve the present system of taxonomic literature.

One of the objectives of pro-iBiosphere is to promote and increase cooperation between the major biodiversity projects, initiatives and platforms at EU and global level (for additional objectives please see persisting traditional workflow for producing taxonomic information, such as Floras and Faunas, is a very time-consuming process for most institutes (i.e. Natural History Museums, Herbaria, Botanic Gardens, etc.). These institutions have the responsibility to make sure that data are generated, curated and disseminated, and that technical operations are working adequately. An Open Biodiversity Knowledge Management System would not only facilitate the open access of taxonomic data, but it would create synergies with other initiatives / projects and through this allow to link taxonomic data in a wider context. These linkages will also offer many means of enhancement for the authors of this taxonomic information.

Examples of European e-infrastructure initiatives include EDIT, BHL-E, BioCASE, ViBRANT, PLAZI, biowikifarm, Pensoft, diversity workbench, BioVeL, and PESI. Over the last years a great number of software platforms have been developed with different functional scopes, content scopes, strengths and weaknesses. Biodiversity informatics infrastructures were often developed as database-driven web-applications which were later equipped with services for machine to machine communication. True interoperability is still hindered by a lack of data standards, standard protocols and solid service implementations.

Pro-iBiosphere will conduct four pilot studies ( and organize six meetings with stakeholders ( ; The FUB-BGBM and Plazi will be responsible for the pilot on "Interoperability model between PLAZI and the EDIT Platform for Cybertaxonomy based on transformations between XML-repositories and CDM-stores".  Main focus will be optimized information- and workflows associated to mobilization, storage and publication of data from biodiversity literature. This includes the review of the existing system, working interfaces, successfully shared standards. The pilot implementation will be used as a proof of concept and establish a transformation pipeline between data from PLAZI (XML-based repositories) and the CDM-stores of the EDIT Platform for Cybertaxonomy (highly granular object-oriented data stores). The pilot will provide both human readable and web-service access to the Plazi data.

With the aim of identifying issues hindering true interoperability (e.g. lack of standards and different conceptual models etc.), a workshops on "How to improve technical cooperation and interoperability at the e-infrastructure level" will take place on October 8-11, 2013, in Berlin ( The workshop will bring together IT- experts and representatives of e-infrastructures, data providers, and scientific users to identify the technical constraints and problems in the interoperability between platforms.  Main outputs of the workshop are: (i) to specify workflows for importing mark-up documents into e-platforms, and (ii) a proposal of optimal solutions that will account the "different start" approach implied by the various stakeholder groups.

Eckert, S., Kelbert, P.,  Güntsch, A., Berendsohn, W. G. Botanischer Garten und Botanisches Museum Berlin-Dahlem Freie Universität Berlin (FUB-BGBM) & Sierra, S. Naturalis Biodiversity Center Leiden

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This project has received funding from the European Union’s Seventh Programme for research, technological development and demonstration under grant agreement No 312848