Virtual Biodiversity ViBRANT Data publishing Lyubomir Penev, Vince Smith, Dave Roberts, Pavel Stoev ViBRANT Virtual Biodiversity “BioFresh goes Political” April 15-19th, 2013 Schloß Machern, Leipzig, Germany

Virtual Biodiversity ViBRANT 2 of Who we are 3 The Natural History Museum, London (NHM) - Scratchpad VRE development & management Hellenic Center for Marine Research, Crete (HCMR) - Extension into ecol.,con. & citizen science, esp. marine biodiversity Royal Belgian Institute of Natural Sciences (RBINS) - Training, outreach & community support Oxford e-Research Centre (UOXF.E9) - Mol. ID tools, services and data analysis Vrije Universiteit Amsterdam (VU) - User studies (sociological studies of user practices) Julius Kühn-Institute (JKI) - Data integration via controlled vocabularies & ontologies Museum für Naturkunde, Berlin (MFN) - Biodiversity inventorying & monitoring (mobile devices) University of Amsterdam (UvA) - Standards development (PESI) The Open University (OU) - Data mining and bibliographies (BHL) Karlsruher Institut für Technologie (KIT) - Document Markup & natural language text processing Vizzuality (Vizz) - Data visualisation & analysis (data layers) Pensoft Publishers (PENSOFT) - Push-button manuscript submission from the Scratchpad VRE Université Pierre et Marie Curie-Paris 6 (UPMC) - Morphological identification keys and services (Xper 2 ) Global Biodiversity Information Facility (GBIF) - Controlled vocab. dev. & userbase expansion via GBIF nodes Freie Universität Berlin (BGBM) - Data aggregation portal via CDM Université de la Réunion (UdlR) - Mathematics & HCI of taxonomic identification keys University of Trieste - Key2Nature integration & outreach 17 partners, 9 countries LifeWatch - prototype service centre ELIXIR - taxonomic metadata services EMBRC - marine model organism research ESFRI collaboration… Wider collaboration… GBIF - thesauri, nodes & data recording PESI, 4D4Life & related EU projects EOL, CBoL & BHL SANBI & Atlas of living Australia 2,392 core users 192 biodiversity communities Tens of thousands through partner networks Current users Biodiversity scientists Professional “amateurs” Citizen scientists Audience

Virtual Biodiversity ViBRANT 3 of Data publishing becomes increasingly important and already affects the policies of the world’s leading science funding frameworks and organizations. The concept of “open data” is described in the Protocol for Implementing Open Access Data, the Open Knowledge/Data Definition, the Panton Principles for Open Data in Science, and the Open Data Manual. 27

Virtual Biodiversity ViBRANT 4 of White House Office of Science and Technology Policy (OSTP) created the Big Data Research and Development Initiative started 29 March 2012 Directive of the Council of Europe recognising “the strategic importance for Europe’s scientific development of open access to scientific information” On 17th July 2012, the European Commission outlined measures to improve access to scientific information produced in Europe in a Communication and a Recommendation to the Member States. 27

Virtual Biodiversity ViBRANT Why do we need to publish our data?

Virtual Biodiversity ViBRANT Primary data Drawings: Slavena Peneva Publishing and sharing of primary data RE-USE of CONTENT

Virtual Biodiversity ViBRANT 7 of open data increases transparency and the overall quality of science published data can be verified by other researchers it can be integrated with other datasets it increases the potential for interdisciplinary research duplication of data-collecting efforts and associated costs will be reduced published data can be indexed and made discoverable 27

Virtual Biodiversity ViBRANT 8 of What is a Data Paper? A Data Paper is a scholarly journal publication whose primary purpose is to describe a dataset or a group of datasets, rather than to report a research investigation. 27 Its purposes are three-fold: to provide a citable journal publication that brings scholarly credit to data publishers; to describe the data in a structured human-readable form; to bring the existence of the data to the attention of the scholarly community.

Virtual Biodiversity ViBRANT 1.Supplementary data files downloadable from the journals website 2.Data deposited at specialized data repositories (Dryad, Pangaea) 3.Data published through data repositories but indexed and collated with other data (GenBank, GBIF IPT) 4.Data published in the form of marked-up and machine- readable text (XML). Multiple Data Publishing Models

Virtual Biodiversity ViBRANT Key features of BDJ Collaborative article authoring Online peer-review and editing Community peer review; options for “open” and “public” review Standard-compliant (DwC, NLM DTD) Biological Codes compliant article templates Semantically enhanced “articles of the future” Integrated with GBIF, EOL, Dryad Scratchpads, etc.

Virtual Biodiversity ViBRANT PWT is a collaborative article authoring and publishing platform for biodiversity science

Virtual Biodiversity ViBRANT It provides: - templates for different kinds of biodiversity articles - links to external resources - various options for data publishing The missing link! It completes the cycle from writing a manuscript, through its submission, peer- review and editing, to publication and dissemination. And all this within a single online collaborative platform!

Virtual Biodiversity ViBRANT

Virtual Biodiversity ViBRANT Peer-review and publishing PENSOFT JOURNAL SYSTEM (PJS 2.0) COMMUNITY, OPEN, PUBLIC PEER-REVIEW PWT MANUSCRIPT PUBLISHED (XML TEXT + DATA) Authors, Reviewers, Editors, Mentors, Copyeditors XML submission Revisions online ARTICLES Occurr- ence data Taxon names Taxon treatments Plazi Wiki COL Biblio- graphies

Virtual Biodiversity ViBRANT

Virtual Biodiversity ViBRANT

Virtual Biodiversity ViBRANT Demanded by the European Commission and would like access the community view in forming the funding calls under Horizon 2020 White paper on biodiversity informatics – a core product of ViBRANT

Virtual Biodiversity ViBRANT Thank you for your attention! ViBRANT Lyubomir Penev Vince Smith Dave Roberts