Virtual Biodiversity ViBRANT Data publishing Lyubomir Penev, Vince Smith, Dave Roberts, Pavel Stoev ViBRANT Virtual Biodiversity “BioFresh goes Political”

Virtual BiodiversityViBRANT

Data publishing

Lyubomir Penev, Vince Smith, Dave Roberts, Pavel Stoev

ViBRANTVirtual Biodiversity

“BioFresh goes Political”

April 15-19th, 2013 Schloß Machern, Leipzig, Germany


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Who we are

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• 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 (Xper2)• 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


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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.

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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.

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Why do we need to publish our data?


Primary data Drawings: Slavena Peneva

Publishing and sharing of primary data

RE-USEof

CONTENT


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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

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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.

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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.


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


Key features of BDJCollaborative article authoringOnline peer-review and editingCommunity peer review; options for “open” and “public” reviewStandard-compliant (DwC, NLM DTD)Biological Codes compliant article templatesSemantically enhanced “articles of the future”Integrated with GBIF, EOL, Dryad Scratchpads, etc.


PWT is a collaborative article authoring and publishing platform

for biodiversity science


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 BiodiversityViBRANTPeer-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

ARTICLESOccurr-

ence data Taxon namesTaxon treatments

Plazi Wiki COL

Biblio-graphies




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


Thank you for your attention!

http://pensoft.netViBRANT

Lyubomir Penev

Vince Smith Dave Roberts

Documents

Virtual Biodiversity ViBRANT Data publishing Lyubomir Penev, Vince Smith, Dave Roberts, Pavel Stoev ViBRANT Virtual Biodiversity “BioFresh goes Political”