GBits

no. 40 Aug 2014

free and open access to biodiversity data

CSIRO’s Tony Rees named
2014 Ebbe Nielsen Prize winner

SCIENCE.. . . . . . . . . . . . . . . . . . . 1
Tony Rees wins Ebbe Nielsen Prize2013 Young Researchers Awards
GBIF publishes 2013 Science Review

DATA PUBLISHING � � � � � � � � � � � 2
Bringing species records to life
Version 2.1 of the IPT released

GOVERNANCE � � � � � � � � � � � � � � � 3Community consultations on
endorsement and data licensing
Registration open for GB21 in New
Dehli

CAPACITY BUILDING � � � � � � � � � 3
Mentoring project updates

NEW DATA � � � � � � � � � � � � � � � � � � 4
BrazilChinese Academy of Sciences
Colombia

GBIF has awarded the 2014 Ebbe Nielsen Prize to
Tony Rees, whose ground-breaking informatics tools
have significantly advanced the delivery of data aboutlife on Earth.
Rees is manager of the marine research data centre
at Australia’s Commonwealth Scientific and Industrial
Research Organisation (CSIRO). He will receive the€30,000 Ebbe Nielsen Prize at GBIF’s 21st Governing
Board Meeting (GB21), which takes place this year in
New Delhi, India, from 16-18 September.
The GBIF Science Committee awards the annual prize toresearchers combining biosystematics and biodiversity
informatics research in an exciting and novel way. GBIF’s
Australian delegation nominated Rees in recognition offour innovative achievements that have advanced global
progress in biodiversity informatics...
read more News release

Denmark
Germany
The Netherlands
United States

AROUND THE NETWORK � � � � � � 5
OPPORTUNITIES � � � � � � � � � � � � 8
COMINGS AND GOINGS � � � � � � 8
EVENTS � � � � � � � � � � � � � � � � � � � � 9
Meetings and conferences
Training courses

To subscribe to the GBits newsletter, visit
www.gbif.org/newsroom/summary#signup
or email info@gbif.org

GBits2013 Young Researchers Awards

This year’s GBIF Young Researchers Awards havegone to a master’s student from Ireland helping
to detect biases and identify gaps in biodiversity
data and a PhD student from India looking at thepotential for social networking sites to provide
valuable biodiversity data.

subject areas including:invasive species,
climate impacts, humanhealth, ecosystemservices, biodiversity
conservation, andfood, farming andbiofuels. Selectedsummaries highlightresearch that either
makes substantial
use of GBIF-mediateddata or reflects key
areas of interest for thescientific and policy
communities.
The GBIF Secretariat maintains an ongoingprogramme of monitoring scientific literature thatuses and discusses GBIF-mediated data. Web users
can access an ongoing historical archive of suchresearch citations.

The winners are Caoimhe Marshall of University
College, Dublin (above left), and Vijay Barve, a
research fellow at the Foundation for Revitalisationof Local Health Traditions (FRLHT) in Bangalore, anda PhD candidate at the University of Kansas, UnitedStates. Both receive a €4,000 prize in recognitionof their research innovation and originality,
the potential for significant contributions tobiodiversity science, and the creative use of data
published through GBIF.
Marshall’s research project aims to validate astatistical method of estimating the relative amountof effort spent on recording species in different
locations, based on data available through GBIF.
Meanwhile, Barve will investigate whether images
shared on sites such as Flickr, Facebook andPicasaweb may be untapped sources of very large
volumes of photo-vouchered species occurrencedata, especially in developing countries.
read more YRA winner Caoimhe Marshallread more YRA winner Vijay Barve

GBIF publishes 2013 Science Review

GBIF has released its annual compilation of peerreviewed research that make use of data publishedthrough GBIF’s global infrastructure.
This issue of the Science Review accounts formore than 250 scientific papers across a range of2

2

download GBIF’s 2013 Science Review

DATA PUBLISHING
Bringing species records to life

Users of GBIF.org can now search for and filter
species occurrences that include visual andacoustic records. GBIF.org’s index now displays
more than 1.5 million species occurrences withphotos, sound or video.
The new multimedia filter increases visitors’ ability
to access more of the detailed information that
accompanies individual records published on GBIF.
org. In addition to highlighting the practical powerof digital media to document species, charismaticor otherwise, these improvements support practicalapplications that advance and extend the work ofscientific researchers.
“Multimedia collections offer important tools
for studying biodiversity, particularly given
improvements in field techniques that make itpossible to automate biodiversity inventory andmonitoring,” said Dr. Karl-Heinz Frommolt, curatorof the Animal Sound Archive at the Museum fürNaturkunde in Berlin.
read more News releaseAug 2011

no. 40 Aug 2014

Version 2.1 of the IPT released

Developers at the GBIF Secretariat released version
2.1 of the Integrated Publishing Toolkit (IPT) in
April. The Release Notes outline the 11 user-driven
enhancements and 38 bug fixes that comprise thisupdate, including key changes that•••

Enable publishers to validate that each record
within a dataset has a unique identifier (thereby
improving stability of record-level identifiers
across the GBIF network)
Support Microsoft Excel as native data sources
Translate the interface into Japanese, courtesyof Dr Yukiko Yamazaki from the National
Institute of Genetics
read more GBIF Developer Blog
read more IPT User Manual

GOVERNANCE
Community consultations on
endorsement and data licensing

Interior, Indian Habitat Centre. Photo 2011 CC BY-NC-ND, Phillip
Kalantzis Cope (flic.kr/p/9nQa4J)

Registration open for GB21 in New Dehli
Official delegates and invited observers canregister now to attend the 21st meeting of the GBIF
Governing Board (GB21), co-hosted by the Wildlife
Institute of India and the Ministry of Environment,
Forests and Climate Change at the India Habitat
Centre (above) in New Delhi from 16-18 September.

The GBIF Secretariat closed a pair of community
consultations in June after receiving input on two
sets of proposed changes to GBIF processes foradding publishers to the network, and for licensing
data mediated by the network.

On 17 September, the public Science Symposium—
entitled Innovation and Impact through GBIF—takes
place, and citizens and journalists can register andattend for free. Look for an announcement on thisyear’s list of speakers in early August.

The endorsement consultation examined an
expansion of the current model for publisher
endorsement that, by engaging expert
communities, could provide a richer assessment of
the value of each dataset to potential users, as well
as facilitating publication of data from institutions
in countries not currently participating in GBIF.

read more Event details for GB21

The consultation on data licensing followed up on a2013 consultation that stems from GBIF’s mission topromote free and open access to biodiversity data.
This proposal outlined a standardized approachthat would make datasets’ terms of use and re-use
restrictions clear to users.
The Secretariat has analysed and summarized
the responses to both consultations in public
documents, and will present proposals for the way
forward on both issues to the GBIF Governing Board
at September’s GB21 meeting in New Delhi, India.
read more Report on endorsement 		
consultation
read more All endorsement responses
read more Report on licensing consultation
read more All data licensing responses

CAPACITY BUILDING
Mentoring project update
France, Portugal and Spain

Staff from GBIF’s national nodes in France, Spain
and Portugal held the second meeting of their joint
mentoring project at the Instituto de InvestigaçãoCientífica Tropical in Lisbon from 28 to 30 April.
Working topics included• creating data papers using GBIF’s Integrated
Publishing Toolkit• preparing e-learning courses• journal options and requirements for publishingdata papers• exploring challenges and opportunities forother nodes that wish to make use of the Atlasof Living Australia’s ALA-portal code
• cleaning biodiversity data using Open Refine
The group will reconvene in Paris on October 14-16
to explore a crowdsourcing platform for cataloguingcollections, and tools for spatial visualization of
biodiversity data, developed by GBIF France.
read more Event materials

33

GBitsMentoring project update
Belgium, Mauritania, and Togo

The GBIF national nodes from Togo, Mauritania
and Belgium co-organized a data workshop at the
University of Lomé, Togo on 18-19 June 2014.
About 25 Francophone participants from Togolese
academic and government institutions took
advantage of this opportunity to learn about GBIF,
the open data movement, data publishing and use,
and fitness-for-use.
Following this more public gathering, IT staff fromthe three nodes began a hands-on collaboration
around how to prepare and publish data throughthe GBIF IPT. Participants published two datasets—
one a checklist of Togolese snakes and reptiles, theother occurrences of West African mushrooms—
and began preparing several more datasets for
publication. Attendees plan a follow-up workshop
in Nouakchott, Mauritania, in early September.

NEW DATA
BrazilThe Brazilian Biodiversity Information System(SiBBr), the GBIF national node for Brazil, hasmobilized the first published data from the Museu
Paraense Emílio Goeldi in Belém. Representing
just a small fraction of collections of Amazonian
biodiversity dating to the 19th century, the ten
initial datasets encompass more than 30,000
records, including 22,000 from the museum’s
collection of Araneae, the world’s second mostdiverse group of spiders.
SiBBr has also facilitated publication of the firstdata from the National Institute of Amazonian
Research (INPA) in Manaus. The appearance of its
first two datasets on GBIF.org marks a milestone
in INPA’s long-term commitment and investment indigitization, infrastructure and publication that will
increase access to its research collections.

Chinese Academy of Sciences

The Biodiversity Committee, Chinese Academyof Sciences has published the first portion of its
historic plant collection through GBIF.org. Thisdataset consists of 163,199 species occurrence
records drawn from various localities in Yunnan
province in southwest China, one of the country’s
hotspots of biological diversity. These data are the44Type specimen of Pleurospermum arometicum, collected by Scottish
botanist George Forrest in Lijiang, Yunnan, in 1910. Photo courtesy ofChinese Academy of Sciences.

first published by the Chinese Academy of Sciences
through GBIF.org since joining the global network in
October 2013 as an associate Participant.
read more News release

Colombia

Working with the Colombian Biodiversity
Information System (SiB), Fundación Bosquesy Humedales has published just over 2,000
records of striped catfish (Pseudoplatystoma
magdaleniatum) in the Magdalena-Cauca basin.
These data establish a baseline understanding
for this newly described endemic species, which
inhabit a basin rich in both Andean and Caribbean
ecosystems.
SiB also endorsed publication of 1,200 beetle
records from the Museum of Natural History Luis
Gonzalo Andrade at the Universidad Pedagógica
y Tecnológica of Colombia. These initial data
represent a small portion of the Museum’s
specimens, nearly 40% of which come from theorder Coleoptera.

Aug 2011

Denmark

DanBIF has facilitated publication of a dataset
collected by citizen scientists for the Natural History
Museum of Denmark. Children, adults, students
and museum researchers worked together tocollect the 582 records during a one-day Bioblitz inØstre Anlæg, a public park in central Copenhagen.
Researchers and experts associated with theMuseum identified all 342 species and recorded
them in a purpose-built registration system.

Germany

In its role as the German node for vertebrate data,
the Zoological Research Museum Alexander Koenig,
Bonn has published a large collection of more than
150,000 bat banding records dating from 1900 to
the present.

no. 40 Aug 2014

United States

An initial set of 85,000 records from fourcollections at the North Carolina State Museum of
Natural Sciences has rapidly grown to comprise
216,000 of its specimens across eight collections.

AROUND THE NETWORK
Ireland’s BioBlitz 2014 highlights
NBDC’s citizen science outreach

Ireland’s annual BioBlitz took place on 23-24
May, with the National Biodiversity Data Centre
convening more than 200 scientists and recorders
at four sites across the island of Ireland to see
which site would record the most species during a
24-hour period. As the largest event of its kind inEurope, the BioBlitz provides citizen scientists andprofessionals a valuable opportunity to networkand exchange skills.
This year, volunteers at Glenarm Estate in County
Antrim logged 1,116 species, surpassing theother three sites at Howth Head in County Dublin,
Derrynane National Historic Property in County
Kerry, and Clonbur/Cong Woodland in County
Galway. The BioBlitz was supported by a dynamic
real-time record capture system, developed by
the Data Centre as an online record submission
and management system that support the citizen
science network in Ireland. The system hasrecorded more than 80,000 records from membersof the public to date.
read more BioBlitz 2014
read more NBDC Record Submission

The FLORIVON dataset includes 51 occurrences from the genus Ophrys,commonly known as ‘bee orchids’. Photo © 2011 Jurgen Rotteveel.

The Netherlands

The Dutch Foundation for Botanical Research(FLORON) has published its FLORIVON dataset,containing nearly 600,000 observations of vascularplants collected during a nationwide survey
conducted primarily between 1901 and 1949. The
dataset is expected to grow as more of the records
are digitized.

GBIF Norway seeks volunteers fortranscribing labels

GBIF Norway launched a new citizen science
crowdsourcing effort at a party marking the200th anniversary of the Natural History Museum
botanical garden in Oslo. Volunteers have beenasked to provide assistance in transcribing themuseum’s thousands of records for African lichen
specimens.
volunteer Lichens of Africa

55GBitsRegional nodes meetings

GBIF’s 2014 work programme includes funding
to support regional node meetings to advancethe network’s shared priorities. Four of GBIF’s six
regions have held their 2014 node meetings, andthe Latin American Participants are set to convene
later this year in Petrópolis, Brazil. Below are somebrief summaries of the recently completed meetingsin Africa, Asia, Europe and North America.

GBIF in Africa
13 African Participants attended GBIF’s 5th African
regional nodes meeting in Cotonou, Benin in July.
Supported by the Faculty of Agricultural Scienceof the University of Abomey-Calavi, GBIF Benin,
and the Benin Ministry of Environment, thegathering occurred on the heels of the first GBIF
African Science Committee meeting as well as thethird workshop of the regional collaboration on
Mobilising Africa’s policy-relevant biodiversity data
(see below).
After highlighting new projects around data
repatriation, alien invasive species and biodiversity
in cities, attendees discussed nine previously
adopted regional priorities for data mobilization,and established collaboration agreements foradvancing toward shared goals. Node staff
outlined the steps necessary to set up an African
coordination mechanism for GBIF-related activities
and appointed leaders to ensure progress on
engagement, informatics, and content to align workin Africa with GBIF’s strategic plan.

GBIF in Asia
Organized by JBIF, GBIF’s Japanese node, the
5th Asian nodes meeting took place in Tsukuba,
Ibaraki, Japan, hosted and funded by the National
Museum of Nature and Science.
The eight participating nodes and one observer
discussed progress to date on current regional
science-based projects. The first will leverage
FishBase, one of the region’s most comprehensive
checklist databases, to improve documentation
on both marine and freshwater fishes across theregion, focusing first on ASEAN countries, theirlocal languages and species occurrences.
The second seeks to mobilize checklist data on
invasive and Red List species, again focusing
initially on ASEAN countries. While the task will
require some outside taxonomic expertise, theAsian nodes expect to provide self-sustaining
support through data analysis, data comparisons
66.......

and other informatics techniques and procedures.
The Asian Nodes will collaborate with the GBIF
Secretariat to improve the GBIF taxonomic
backbone and to increase the services to compare
and synchronize country checklists (e.g. correctionof errors in names).
The nodes also held elections, voting in Tsuyoshi
Hosoya of GBIF Japan as the new Asian nodes
representative and Yu-Huang Wang of TaiBIF as
the deputy representative. The pair succeed Sheila
Vergara of the Asian Centre for Biodiversity andNakul Chettri of ICIMOD, for whose service the GBIF
network is very grateful.

GBIF in Europe
Around 40 staff from 24 GBIF participants attendedApril’s 6th European Nodes meeting in Brussels,with support from the Belgian Biodiversity
Platform and the Belgian Federal Science Policy
Office. In the course of sharing updates on several
EU-related projects and initiatives, attendees
analysed lessons learned from previous regionaland global collaborations on invasive freshwater
data mobilization, the Nodes Portal Toolkit andmentoring collaboration.
Node managers and staff also identified a set of
regional priorities, which include engaging potential
new members in Eastern Europe to increase GBIF’s
coverage, mobilizing content that closes regional
data gaps and through large-scale digitization, andconnecting other biodiversity informatics initiatives
across the continent. Some nodes agreed to a joint
focus on publishing European forest and vegetation
data in support of the European Environment
Agency.

GBIF in North America
The North American region held its fourth meetingin Guelph, Canada, with support of the International
Barcode of Life and the Biodiversity Institute ofOntario. On-site and dial-in attendees discussed
current project news and how adjustments to theregion’s governance model might stimulate further
regional collaboration. The implications of the
Nagoya protocol for collections and data licensing,
the need for unique identifiers for records, andmodels for including other information through
GBIF—such as both genetics and sample-based
data—formed key topics of conversation.
The North American nodes also re-elected Bob
Hanner as their representative for another two-yearterm.

Aug 2011

African Participants flesh out a businesscase for mobilising biodiversity data
More than 20 African experts convened on 1 Julyat Hotel Pantagruel in Cotonou, Benin, to design a
training programme and build a business case formobilizing policy-relevant biodiversity data. The
workshop occurred between meetings of the GBIF
Africa Science Committee (30 June 2014) and the
GBIF Africa Nodes Committee (2-4 July 2014).

The South African National Biodiversity Information
Facility (SABIF) coordinated the workshop, the third
in a series to support Mobilising Africa’s policyrelevant biodiversity data, a project funded by the
JRS Biodiversity Foundation that draws together
GBIF’s African Participants. The project’s goal is todevelop and implement a strategy for mobilizing
African biodiversity data while strengthening
regional collaboration and capacity in biodiversity
informatics.
Workgroups sought to design pragmaticcomponents of a biodiversity informatics training
programme, seeking to alleviate chronic capacity
constraints and streamlining the ‘data-sciencepolicy value chain’. The agenda included apresentation by Nadine Bowles-Newark of UNEPWCMC and concluded with participants discussing
the prospect of organizing a major African datascience-policy conference in 2015.

no. 40 Aug 2014

AnnoSys has been integrated and deployed within
the Virtual Herbarium Berolinense, the SYNTHESYS
portal for European biodiversity data and the EDIT
Specimen Explorer.

Language group news
Français, Español and Português

The collaborative work of translating recent
community consultations has generated a welcome
side effect: the creation of glossaries of the mostcommon GBIF and biodiversity informatics terms in
French, Spanish and Portuguese.
While still a work-in-progress, the glossaries havealready streamlined the process of communicating
within and across the tongues that make up the
GBIF network. Secretariat staff sincerely thank themembers of the community who have made suchinvaluable contributions to these efforts.
read more Glossaire Anglais > Français pourles termes utilisés par le GBIF
read more Diccionario inglés > español parala informática de la biodiversidad
read more Glossário inglês > português paraa informática da biodiversidade

Global marine datasets for species
distribution modelling and visualization

National data resource launched in
Benin

GBIF Benin worked closely with INBio (Costa Rica’s
national node) to create a new national portalthat displays GBIF-mediated data in a single
resource. Developed with support from the JRS
Biodiversity Foundation, gbif-benin.org is a Drupal
implementation based on the NPT Startup.

BGBM launches system for annotating
biodiversity data

The Botanic Garden and Botanical Museum
Berlin-Dahlem (BGBM) has released a new systemthat enables the addition of online comments tobiodiversity data.
The AnnoSys annotation data repository allows
users to identify and propose corrections to errors
and omissions in occurrence records. For eachannotated record, the AnnoSys repository stores
both the annotation and the original record, linking
them through a persistent identifier. These records
are accessible through the AnnoSys user interface
and web service interfaces.

The Global Marine Environment Datasets (GMED)
is a compilation of global climatic, biological, andgeophysical environmental layers for the current,
past and future conditions of marine environments.
Covering a wid range of environmental layers
from the surface and the deepest oceans, GMED
provides standardized, ready-to-use datasets withuniform spatial extent at high spatial resolution (5arc-minute, c. 9.2 km near equator).

7

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GBits“Researchers can map GBIF-mediated data against
these layers to quickly visualize environmental
context for species distributions,” says Mark
Costello of the University of Auckland’s Leigh
Marine Laboratory (and vice-chair of the GBIF
Science Committee). “MaxEnt and other species
distribution modeling software can also import
GMED to generate predictions of the geographic
ranges of species and regions where, if introduced,
a given species might find suitable conditions.”
read more Global Marine Environment
Datasets

OPPORTUNITIES
Vacancies at BeBIF

The Belgian Biodiversity Platform (BeBIF), the GBIF
national node for Belgium, is seeking to fill two
positions, one full-time and one part-time. BeBIF
is a science-policy interface based in Brusselsthat provides services to scientists engaged inbiodiversity research and policy makers,
read more Science Officer for biodiversity
science-policy communication (full-time)read more Biodiversity Expert for sciencepolicy interface issues (part-time)

CESAB issues call for proposed proposals
CESAB (the Center for Synthesis and Analysis on
Biodiversity), which funds high-level biodiversity
research, has launched its annual call for research
project proposals.

An initiative run by the French Foundation for
Research on Biodiversity, CESAB offers to funding
support of expert groups with resources andinfrastructure to share datasets and conduct
extensive investigations on biodiversity-related
concepts. Projects are generally funded for a threeyear period and must not require the collection of
new primary data. Deadline for pre-proposals is 16
September 2014.
read more Call for presentations (English)

COMINGS AND GOINGSThe GBIF Secretariat has added three staff in recent
months with another pair to follow shortly.

8

8

Dr Siro Masinde will join
the Secretariat at the
beginning of September
as the new programme
officer for content
mobilization. As seniorresearch scientist andpreviously as head of
the botany department
at the National
Museums of Kenya,
which includes the East
African Herbarium and Nairobi Botanic Garden.
Siro has extensive experience in digitizationand databasing, including as African regional
coordinator for JSTOR/ITHAKA, for which he helped
develop the Global Plants Initiative.
In mid-October,
Dr Dmitry Schigel
will join as the
new programme
officer for content
analysis and use.
A Russian currently
working in Finland,
Dmitry is adjunctprofessor (docent)in mycology at
the University of
Helsinki. He also
acts as taxonomy coordinator for the ICT team at
the Finnish Museum of Natural History, host of the
GBIF national node for Finland, and runs a research
project on wood-decaying fungi for the university’s
Metapopulation Research Group.
Meanwhile, Maheva Bagard Laursen has joinedas Communications Officer as a maternity-leave
replacement for Sampreethi Aipanjiguly, whowill return in February 2015. Maheva has worked
in communications, networking and project
management in Europe and in China, most recently
as an outreach communication consultant at theEuropean Environment Agency (EEA). Maheva
will be the main contact point for suggested
contributions to GBits in coming months and canbe reached at mblaursen@gbif.org and via Skype atmahevalaursen.

Aug 2011

no. 40 Aug 2014

Kyle Copas started
as the Secretariat’s
science writer in May,
focused on creating
content for GBIF.org andother communication
platforms, as well ascrafting and leading
implementation of
GBIF’s communication
strategy. Kyle contributes experience acrossthe realms of biodiversity conservation andsustainability, having spent the past sevenyears in a variety of content, communications,and strategy roles at NatureServe, a U.S.-based
associate Participant in the GBIF network. Kyle canbe reached at kcopas@gbif.org and via Skype atkylecopas.

EVENTS

Finally, Marlene
Dalsgaard Nielsen
started March 1 as
the Secretariat’s
administrative assistant.
Trained at the Ministryof Foreign Affairs in
Copenhagen, Marlene
worked at the Royal
Danish Embassy andEuropean Medicines
Agency (EMA) in London,and most recently worked
in Copenhagen for Novo
Nordisk. She can bereached at mdnielsen@gbif.org.

2014 TDWG Conference
27-31 October 2014, Jönköping, Sweden

Meetings and conferences

Scientific Committee on Arctic Research (SCAR)
2014 Open Science Meeting
27-28 August 2014, Auckland, New Zealand4th GBIF Latin American Nodes Meeting
1-3 September 2014, Rio de Janeiro, Brazil
2014 ALTER-Net summer school: ‘AnInterdisciplinary Perspective on Biodiversity andEcosystem Services’
3-13 September 2014, Peyresq, France
GB21: 21st GBIF Governing Board Meeting
16-20 September 2014, New Delhi, India
COP12: Conference of the Parties to the CBD
3-17 October 2014, Pyeongchang, Republic of Korea

IUCN World Parks Congress
12-19 November 2014, Sydney, Australia
2nd International Ocean Research Conference
17-21 November 2014, Barcelona, Spain
Arctic Biodiversity Congress
2-4 December 2014, Trondheim, Norway

Training courses

Spatial Conservation Planning with Marxan
18-22 August 2014, Els Hostalets de Pierola, Spain
Biodiversity Diagnoses Course
1-9 September 2014, Cotonou, Benin

GBIF Vision A world in which biodiversity information is freely and universallyavailable for science, society, and a sustainable future.
GBIF Secretariat
Universitetsparken 15
DK-2100 Copenhagen Ø
Denmark
http://www.gbif.org/

Tel+45 35 32 14 70
Fax+45 35 32 14 80
Email info@gbif.org
GBits Archive http://www.gbif.org/newsroom/newsletter
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