Transcript BIOFRESH_meeting_2013

“BioFresh goes Political”
ViBRANT
Virtual Biodiversity
ViBRANT
Virtual Biodiversity
Data publishing
Lyubomir Penev, Vince Smith,
Dave Roberts, Pavel Stoev
April 15-19th, 2013 Schloß Machern, Leipzig, Germany
ViBRANT
Virtual Biodiversity
Who we are
17 partners, 9 countries
• The Natural History Museum, London (NHM)
• Université Pierre et Marie Curie-Paris 6 (UPMC)
- Morphological identification keys and services (Xper2)
- Scratchpad VRE development & management
• Hellenic Center for Marine Research, Crete (HCMR)
• Global Biodiversity Information Facility (GBIF)
- Extension into ecol.,con. & citizen science, esp. marine biodiversity
• Royal Belgian Institute of Natural Sciences (RBINS)
- Controlled vocab. dev. & userbase expansion via GBIF nodes
• Freie Universität Berlin (BGBM)
- Training, outreach & community support
• Oxford e-Research Centre (UOXF.E9)
- Data aggregation portal via CDM
• Université de la Réunion (UdlR)
- Mol. ID tools, services and data analysis
• Vrije Universiteit Amsterdam (VU)
- Mathematics & HCI of taxonomic identification keys
• University of Trieste
- User studies (sociological studies of user practices)
- Key2Nature integration & outreach
• 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)
Audience
• Biodiversity scientists
• Professional “amateurs”
• Citizen scientists
• 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
ESFRI collaboration…
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LifeWatch - prototype service centre
ELIXIR - taxonomic metadata services
EMBRC - marine model organism research
Current users
• 2,392 core users
• 192 biodiversity communities
• Tens of thousands through partner networks
Wider collaboration…
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GBIF - thesauri, nodes & data recording
PESI, 4D4Life & related EU projects
EOL, CBoL & BHL
SANBI & Atlas of living Australia
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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
scientific information”
 On 17th July 2012, the European Commission outlined
measures to improve access to scientific information produced
Europe in a Communication and a Recommendation to the
States.
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Why do we need to publish our data?
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RE-USE
of
CONTENT
Publishing and sharing of primary data
Primary data
Drawings: Slavena Peneva
ViBRANT
Virtual Biodiversity
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.
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.
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Multiple Data Publishing Models
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).
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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.
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PWT is a collaborative article
authoring and publishing platform for
biodiversity science
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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!
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Peer-review and publishing
XML
submission
PWT
Revisions
online
Authors, Reviewers, Editors, Mentors,
Copyeditors
ARTICLES
Bibliographies
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PENSOFT JOURNAL SYSTEM
(PJS 2.0)
COMMUNITY , OPEN, PUBLIC
PEER-REVIEW
MANUSCRIPT PUBLISHED
(XML TEXT + DATA)
Occurrence data
Taxon treatments Taxon names
Plazi
Wiki
COL
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ViBRANT
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White paper on biodiversity informatics – a core
product of ViBRANT
Demanded by the European
Commission and would like access
the community view in forming
the funding calls under Horizon
2020
ViBRANT
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Thank you for your attention!
Lyubomir
Penev
Vince Smith
Dave Roberts
ViBRANT
http://pensoft.net