GBits

no. 32 Jan 2013

COLLABORATIONS � � � � � � � � � � 2
GBIF receives €300,000 to assist in Europeanplatform

free and open access to biodiversity data

DATA PUBLISHING � � � � � � � � � � 2
Support for projects to promote ‘data paper’
publication

GBIF ready to support
new science-policy
platform

INFORMATICS � � � � � � � � � � � � � � 2
Duplicate and redundant records cleaned up in
GBIF data portal

SCIENCE AND POLICY � � � � � � 3

The GBIF community has an important role to play insupporting the new Intergovernmental Science-Policy
Platform on Biodiversity and Ecosystem Services (IPBES),
according to executive secretary Donald Hobern.

AROUND THE NETWORK � � � � 3ColombiaBrazil
FranceHobern was speaking after the opening plenary meetingof IPBES which took place in Bonn from 21-26 January.
The meeting put in place many of the administrative andstaffing structures needed to implement its work (see finalpress release at http://www.ipbes.net/).

Denmark
GermanyIreland
CBOLThe GBIF Secretariat issued a briefing note before theBonn meeting outlining the potential areas in which GBIF
had a significant role to play in supporting the IPBES work
programme, which will be drafted during 2013. Those
areas included:• identifying and prioritizing knowledge gaps;• partnerships with long-term observation andmonitoring programmes;• addressing capacity building needs; and• increasing access to data, information and knowledge.

NEW DATA � � � � � � � � � � � � � � � � � � 4Austria
Estonia
IrelandUnited Kingdom
FranceColombia
Netherlands

Alfred Oteng-Yeboah, GBIF Head of Delegation for Ghana, elected as ViceChair of the IPBES Bureau during the plenary meeting in Bonn.

Courtesy of IISD/Earth Negotiations Bulletin

OPEN CALLS � � � � � � � � � � � � � � � � 5

Following the conclusion of the IPBES plenary, Hobern
said: “With the structures and procedures of IPBES now inplace, we look forward to discussing with GBIF Participants,
stakeholders and partners how best we can collaborate
constructively with the new platform.
Continued on page 2...

Call for nominations for GBIF science awards
Call for mentoring activity proposals

IN THE NEWS � � � � � � � � � � � � � � � 6Biodiversity data access project in India ‘to startsoon’
GBIF’s work highlighted in International Innovation

UPCOMING EVENTS � � � � � � � � 6Meetings and workshops
Training events

To subscribe to the newsletter, please contact info@gbif.org

GBits...continued from page 1“A key principle of IPBES is that it will work withexisting initiatives on biodiversity, building on theirwork while avoiding duplication. I believe the GBIF
infrastructure for biodiversity data access, built up
over more than a decade, represents an importantfoundation upon which IPBES can now build.”
During the consultations on the IPBES work
programme in the coming months, GBIF will
work closely with a range of partners including astakeholder group coordinated by the International
Union for the Conservation of Nature (IUCN) andthe International Council for Science (ICSU); as wellas with major data publishers to the GBIF network
such as the Ocean Biogeographic Information System(OBIS), operating under the Intergovernmental
Oceanographic Commission (IOC) of UNESCO.
Submissions to IPBES from OBIS, IUCN and otherorganizations can be downloaded at www.ipbes.net/bonn.

COLLABORATIONSGBIF receives €300,000 to assist inEuropean platform
GBIF is participating in a major new project to build
a European Biodiversity Observation Network, aimedat helping scientists, policy makers and the public toaccess a wide range of biodiversity information.
The EU BON project, funded by the European Union,brings together 30 partners from 18 countries. Thework will cost €9 million, spread over four and a halfyears.
Among the products will be a European integrated
biodiversity portal, a roadmap for handling citizen
science data and a framework for open datapublishing.
GBIF’s specific contributions, costed at nearly€300,000, include helping to improve data standards
and interoperability, providing a metadata registry
and catalogue, and providing access to data throughrobust web services.
EU BON is led by the Museum für Naturkunde,
Berlin, and will contribute to the Group on Earth
Observations Biodiversity Observation Network(GEO BON). An EU BON ‘kick-off meeting’ will beheld in Berlin from 13-15 February, preceded byan international symposium entitled Nature andGovernance – Biodiversity Data, Science, and thePolicy Interface, taking place on 11-12 February.

22DATA PUBLISHING
Support for projects to promote ‘datapaper’ publication
The GBIF Secretariat has announced support for threeco-ordinated projects aimed at promoting publicationof peer-reviewed biodiversity ‘data papers’ in Spain,
Latin America and Asia.
The successful proposals are a response to a callissued last year, to stimulate activities among GBIF
nodes promoting the culture of authoring detailed
dataset descriptions (metadata), and publishing themin academic journals.
In one project, GBIF Spain will hold a workshop on
data paper publication in March involving more than
20 existing and potential dataset publishers in Spain.
It is hoped that each of the participants will be able
to publish a data paper as a result of the workshop.
In addition, the Humboldt Institute’s journal, Biota
Colombiana, will introduce a special section for thepublication of data papers according to the GBIF
model. This will make it the first journal in Latin
America to publish biodiversity data papers.
The final project has been developed by the Wildlife
Institute of India, host of the Indian national node,
which will also hold a workshop to stimulate
publication of data papers, using training material
developed by Spain and Colombia. This is intended
to result in the submission of at least 20 data paper
manuscripts, and publication of new datasets to theGBIF network, from south and southeast Asia.
Each of the three projects will receive catalytic
support of €5000 from GBIF’s core funds.
For more information, please contact Vishwas
Chavan, GBIF Secretariat, vchavan@gbif.org

INFORMATICS
Duplicate and redundant records cleaned
up in GBIF data portal
Sharp-eyed visitors to the GBIF website may havenoticed a drop in the total number of records from389 million to 383 million in December 2012.
The explanation is that software and processing
upgrades have made it easier to spot duplicatesand old versions of records and datasets that are nolonger being published.
The removal of such records cleans up the data
accessible via the GBIF network, thanks to theinformatics tools developed and promoted by theGBIF community.

Aug 2011

Details of the changes are explained by GBIF systems
analyst Andrea Hahn in the GBIF developer blog.
Read more…

SCIENCE AND POLICY
As usual, the current issue of GBits is accompanied
by a supplement summarizing the uses of GBIFmediated data identified in the past two months. The
sixth GBits Science Supplement includes details of astudy projecting the likely impact of climate change
on mammals in the far north of Europe, and the latest
GBIF data paper describing a new survey of mollusc
species on a volcanic island off Taiwan.
Download the supplement …

no 32 Jan 2013

National Secretary for Policies and Programmes at
the Brazilian Ministry of Science, Technology andInnovation (MCTI). The Director of Thematic Policies
and Programmes at MCTI, Mercedes Bustamante, hasbeen designated as Additional Delegate. The national
node will be hosted at the National Laboratory for
Scientific Computation (LNCC), a national research
institution in computer science, linked to the MCTIand located in the city of Petrópolis, in the state of Riode Janeiro. Luiz Gadelha of LNCC will represent Brazilon the GBIF Participant Node Managers Committee.
Contact details can be found on the GBIF website at
http://www.gbif.org/communications/directory-ofcontacts/

FranceAROUND THE NETWORK

Crowdsourcing to help digitize Frenchherbarium collections

Colombia

Citizen ‘herbonauts’ can now contribute to science byhelping to digitize the vast quantity of plant records
held in the National Museum of Natural History(MNHN) in Paris, host of the GBIF national node.

New portal on Colombia’s biodiversity

A portal that provides free access to information on
Colombia’s biological diversity has been launched by
the GBIF national node at http://www.sibcolombia.
net.
The site allows users to explore, filter, access anddownload all specimen records and taxon lists
published by museums, herbaria, universities andgovernment agencies, which are partners of theSistema de Información sobre Biodiversidad (SiB) –Colombia’s biodiversity information facility. Recordscan also be searched at the department level, which isthe second tier of administration in the country.
SiB Colombia created the portal by customizing theopen source tools developed by GBIF. Recycling
the GBIF source code has saved SiB Colombia over
six years of efforts to build a data integration andpublishing platform. The source code for the nationalversion is available at http://code.google.com/p/sibdataportal/.
SiB Colombia has also released a seven-step guide topublishing data on the portal. It is based on a guidedeveloped previously by Canadensys on publishingprimary biodiversity data using the GBIF Integrated
Publishing Toolkit (IPT).

BrazilBrazilian GBIF delegation and node manager
appointed

GBIF’s newest Participant, Brazil, has announced
details of the individuals and national institutions
that will represent the country and coordinate its
participation in the network. The Head of Delegation
to the GBIF Governing Board will be Carlos Nobre,

The French website lesherbonautes.mnhn.fr enables
volunteers to transcribe essential information fromaround six million scanned images of labelled plant
specimens from the museum’s National Herbarium.
It would take a person working alone about 500 years
to enter data from these images. In order to involveand get help from the public, ‘missions’ have been
set up, each with 250-2500 images of specimens.
Volunteers randomly choose images and enter
information from its label.
Digitizing the collections enables data to bepublished, searched and accessed online, contributing
to scientific research. The data from the project will
feed into national databases such as those of theInventaire National du Patrimoine Naturel (NationalInventory of Natural Heritage, INPN) and into
international data networks such as GBIF.
The digitization project is an effort of the MNHN, thefrancophone botanical network Tela Botanica andE-ReColNat, a project to mine biodiversity data in theFrench natural history collections.
Australian volunteers have already been helping todigitize biodiversity data through the Biodiversity
Volunteer Portal, operated by the Atlas of Living
Australia, another GBIF national node.

Denmark
New tool available to manage zoologicalcollections

Papis, a tool developed by the Zoological Museumof Denmark to help manage zoological collections,33

GBitsis now freely available for users. Papis is GBIFcompatible and adds to the suite of software tools
available for managing biodiversity data.
Managing zoological collections involves cataloguing
specimens stored in various forms – such as driedmaterial or in solution, and often accompanied byfield notes, making the process much more complex
than managing plant collections. Papis helps in storing
specimen data, managing specimen loans and keeping
track of maintenance.
Papis is based on FileMaker software. More tools for
managing natural history collections are available on
the GBIF Online Resource Centre.

Germany
Prototype system for annotating biodiversity
data

AnnoSys, a system to enable adding comments tobiodiversity data available via the Internet, is being
tested in prototype by the Botanic Garden and
Botanical Museum Berlin-Dahlem (BGBM), host of theGBIF German node.
The prototype is expected to be available for public
testing in a few weeks, and to be ready for use in April
2014.
AnnoSys will provide a user-friendly interface forresearchers to annotate single datasets as well as setsof collection objects. It will also allow a user to search
for annotations.
The system will help correct errors and rectify
omissions through community input, thus acting as animportant quality control mechanism.
The project is funded by German Research
Foundation (DFG). More information on AnnoSys
is available at https://annosys.bgbm.fu-berlin.de/.
For details, please contact Okka Tschoepe, BGBM ato.tschoepe@bgbm.org.

Ireland
Irish data centre announces 2013 workshops

The National Biodiversity Data Centre, Ireland, has
released its programme of training workshops for2013. A series of 26 workshops will be held thisyear to build capacity amongst the volunteer andprofessional recording community in Ireland on theidentification and recording of the country’s biologicaldiversity.
The programme is devised to provide introductoryand refresher courses for beginners for some of themore popular taxonomic groups, but there are also
more specialist workshops to improve the skills of44

existing recorders.
More on the NBDC website…

CBOL
GBIF partner CBOL wins $3m award from
GoogleThe Consortium for the Barcode of Life (CBOL) has
received $3 million from the Google Global Impact
Awards to create a public library of DNA barcodes for
CITES-listed species.
The Convention on International Trade in Endangered
Species of Wild Fauna and Flora (CITES) is anagreement between governments to ensure thatinternational trade in wild animal and plant species
does not threaten their survival.
CBOL, a GBIF Associate Participant, will work withresearchers in six developing countries, and the DNA
library is intended to be a useful tool for border andcustoms officials in controlling wildlife trade.
Read more…

NEW DATA
Austria
The Austrian Institute of Technology has published21,600 records from its gene repository centre, whichhouses over half a million DNA samples of plant andanimal origin. The centre gives scientists online accessto decoded genetic material from across Europe.
(http://data.gbif.org/datasets/resource/14569)

Estonia
The Estonian Environment Information Centre, astate agency administered by the Ministry of theEnvironment, has published 166,500 records from its
nature observations database. The database gathers
citizen observations of Estonian species and invites
members of the public to input information.
(http://data.gbif.org/datasets/resource/14570)

Ireland
A new dataset published through GBIF includes morethan 31,000 records of marine species observed byvolunteer sports divers around the Irish coastline.
The data, published by the GBIF node at the National
Biodiversity Data Centre, come from the Seasearch
project which offers courses to divers to help them
identify and record marine life.
(http://data.gbif.org/datasets/resource/14563)

FranceThe National Museum of Natural History, Paris has
published nearly 400,000 records of animals, plants

Aug 2011no 32 Jan 2013

United Kingdom
Data from a system to alert UK authorities toinvasive alien marine species are now accessible
through the GBIF network. The UK National
Biodiversity Network has published 121 records ofChinese Mitten Crab, Japanese kelp (Wakame) andCarpet Sea Squirt, all of which are non-native species
whose spread has harmful impacts on local marine
biodiversity. The data come from the Recording
Invasive Species Counts (RISC) and ALERT system,
launched in 2010, and are mostly provided by thepublic through an on-line recording form. Recordsare submitted with a photograph, and only thoseverified by designated experts are included in thedataset. The recordings send a rapid notification tothe Non-Native Species Secretariat, which works tostop their spread.
(http://data.gbif.org/datasets/resource/14568)

and fungi from the public forests of France andCorsica, submitted by staff of the national forest office(Office National des Forêts). The dataset forms part of
the national inventory of natural heritage (Inventaire
National du Patrimoine Naturel, INPN), which
manages and makes available online information on
the terrestrial and marine biodiversity of France andits overseas regions.
(http://data.gbif.org/datasets/resource/14580)

Colombia
The Asociación de Becarios del Casanare, a non-profit
organization based in the Casanare department ofColombia, has published 3,535 records of birds andmammals observed at Laguna Tinije, a lake in theregion. Over 3,400 of these are bird observations
from the dry and rainy seasons of 2009.
(http://data.gbif.org/datasets/resource/14557 andhttp://data.gbif.org/datasets/resource/14559)
Another Colombian non-profit organization,
Asociación Selva, has published 5,250 records ofcaptures and recaptures of banded or ringed birds
in the Sierra Nevada de Santa Marta, a mountain
range near Colombia’s Caribbean coast. Each record
includes detailed information including geographic
coordinates and altitude, the date taken, name of thebander, the number of the band and characteristicsof the individual bird. Banders involved in the study
possess field certificates, ensuring data quality.
(http://data.gbif.org/datasets/resource/14571)

Netherlands
The Royal Dutch Angling Association has published
380,000 records from its Piscaria database, which
is used as the country’s standard for the storage
and analysis of fish data. The dataset includes
common fish species like the European bullhead

Japanese Kelp / Wakame (Undaria pinnatifida)
Photo by Kathryn Birch - CCW

and the northern pike, as well as rare species suchas the brook lamprey, which is threatened in theNetherlands.
(http://data.gbif.org/datasets/resource/14574)

OPEN CALLS
Call for nominations for GBIF scienceawards
GBIF invites proposals for the 2013 Ebbe Nielsen Prizeand Young Researchers Awards.
The €30,000 Ebbe Nielsen Prize is awarded annuallyto a person or team who demonstrates excellence incombining biodiversity informatics and biosystematics
research. Read more…
The Young Researchers Awards are available tograduate students from a GBIF Voting Participant or
Associate Participant country, for innovative researchin biodiversity informatics. Two awards of €4,000 areavailable. Read more…

Call for mentoring activity proposals
The 2013 call for proposals under the GBIF mentoring
programme is now open to GBIF Participant Nodes.
The deadline for submitting proposals is 2 April 2013,
and selected proposals will be announced by the endof April 2013.
The GBIF mentoring programme brings together
GBIF Participant Nodes to share their expertise.
It was designed as a mechanism to speed up theestablishment of biodiversity information facilities inparticipant countries.
More on the 2013 call for proposals…
55

GBitsIN THE NEWS
Biodiversity data access project in India‘to start soon’
The Hindu national daily newspaper in India hasreported that a prototype of the Indian National
Biodiversity Grid, a platform to share open accessdata on the country’s ecosystems, is currently being
tested. The project involves GBIF partners in India,
and follows a recommendation of the draft National
Biodiversity Information Outlook (NBIO) for India,
launched at the Convention on Biological Diversity
meeting in Hyderabad in October 2012.

Eye on Earth network, first user conference
Organized by the European Environment Agency (EEA)
4-6 March 2013, Dublin, Ireland
More information…
European regional nodes meeting
6-8 March 2013, Joensuu, FinlandMore information…
Latin American regional nodes meeting
11-13 March 2013, Santo Domingo de Heredia, Costa
Rica
African regional nodes meeting
16-18 April 2013, Pretoria, South Africa

Read the article here…

Training events

GBIF’s work highlighted in International
Innovation

Training workshops associated with the ‘Capacity
Building for Conservation’ congress
15 February 2013, Villa de Leyva, Colombia
More information…

The Chair of the GBIF Governing Board Joanne Daly,
Executive Secretary Donald Hobern and Senior
Programme Officer for Engagement Tim Hirsch
discuss the challenges and future of GBIF’s work inthe January edition of the magazine International
Innovation – North America.
Read the story…

UPCOMING EVENTS
Meetings and workshops
Biodiversity Information Architecture workshop
4-8 February 2013, Kirstenbosch, Cape Town, South
AfricaHosted by South African National Biodiversity Institute(SANBI)
Symposium: Nature and Governance – Biodiversity
Data, Science, and the Policy Interface
11-12 February 2013, Berlin, Germany
More information…
EU BON kickoff meeting
13-15 February 2013, Berlin, Germany
More information…

Biodiversity data cleaning and data publishing
training course in ICIPE
18-22 February 2013, Nairobi, Kenya
More information…
III Workshop on biodiversity data migration by GBIF
Spain
19-20 February 2013, Madrid, Spain
More information…
Ecological niche modeling course in ICIPE
25-28 February 2013, Nairobi, Kenya
More information…
Global Taxonomy Initiative Capacity-building
Workshop by CBD
4-7 March 2013, Dakar, Senegal
More information…
Training course in biodiversity information
3-28 June 2013, Tervuren, Belgium
Deadline for applications: 15 March 2013
More information…

VISION OF GBIF: A world in which biodiversity
information is freely and universally available forscience, society, and a sustainable future.

MISSION OF GBIF: To be the foremost global resourcefor biodiversity information, and engender smart
solutions for environmental and human well-being.

GBIF Secretariat
Universitetsparken 15
DK-2100 Copenhagen ØDenmark

Tel: +45 35 32 14 70
Fax: +45 35 32 14 80
E-mail: info@gbif.org

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http://www.gbif.org/

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