GBits

no. 35 Jul 2013

INFORMATICS � � � � � � � � � � � � � � 2
GBIF enables new national portals

free and open access to biodiversity data

GBIF mentoring schemesannounced
Three mentoring projects involving eight GBIF Participant
countries will share expertise and experience across the
network, helping to build capacity for publishing and use of
information on biodiversity.
The following projects have been approved and funded
under the 2013 GBIF Mentoring Programme.
• The Information System for Colombian Biodiversity(SiB Colombia) will help its counterpart SiB Brazil toaccelerate the setting up a new Brazilian biodiversity
information infrastructure, following the country’s
entry into GBIF last October.
• GBIF Belgium will mentor Participant nodes in Togo
and Mauritania to improve their capacity to publish
data. The project will also focus on the deployment of
biodiversity information websites in Mauritania andTogo. The Nodes Portal Toolkit Startup, a GBIF product,
will be assessed as a candidate for this.
• In the final mentoring project, GBIF nodes in Spain,
France and Portugal will exchange their expertise indifferent areas, for mutual benefit. GBIF France will use
its experience with a website using crowdsourcing todigitize botanical specimen labels, to support a similarpilot project in Spain and Portugal. France will also
support Spain and Portugal in developing a tool for
visualizing data from their collections, based on tools
developed for the new French data portal. As partof the same project, GBIF Spain will help to set up an
e-learning platform for GBIF France and an e-learning
training package for GBIF Portugal.
Each of the three projects will receive between €8,000 and€15,000 from GBIF’s core funds, which are provided bygovernments of GBIF Voting Participant countries.
Read the full story…

NEW TOOLS � � � � � � � � � � � � � � � � 2
Smartphone apps for plant identification fromimages …
… and for keys to identify insects and invasive
weeds
New Wiki site on thrips

SCIENCE AND POLICY � � � � � � 3
GBits Science Supplement

AROUND THE NETWORK � � � � 3
Call to mobilize biodiversity data from subSaharan Africa
Grants awarded to digitize US biodiversity
collections
New genomics centre in Canada to house DNA
barcoding project

NEW DATA � � � � � � � � � � � � � � � � � � 3
Belgium
Netherlands
FranceGermany
IrelandSwedenUnited Kingdom
CanadaColombia
ZooKeys journal

TRAINING AND
COLLABORATION � � � � � � � � � � � 5
E-learning course on generating data papers
Online forum for biodiversity information in Latin
America and Spain
Georeferencing training in South Africa

GBIF IN THE NEWS � � � � � � � � � 6
UPCOMING EVENTS � � � � � � � � 6
Meetings and workshops
Training events

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

GBitsINFORMATICSGBIF enables new national portals
Three GBIF Participant countries have released newor revised web portals giving citizens and scientists
better access to information about their country’s
biodiversity.
Japan, Portugal and Colombia have all launched orenhanced their national biodiversity information
websites using tools, codes and information sources
developed by the GBIF community.
Since the last issue of GBits:• The GBIF node for Portugal, based at the TropicalResearch Institute (IITC) in Lisbon, has released
a bilingual portal. In its early stages, the site
provides information for the Portuguese-speaking
community on publishing and using biodiversity
data through the GBIF network. In the future, theportal will display occurrence records in Portugal
and data from Portuguese publishers, and help
improve discovery and use of biodiversity datain the country. Open-source functionalities andtools developed within the GBIF network will be
adapted and used for the portal. Read the fullstory in English and in Portuguese.
• GBIF Japan’s portal has been redesigned and
now includes new features such as an online
request form for institutions interested in making
data available through GBIF. It also offers a test
to ensure that the data are compatible with theDarwin Core standard, the principal means oforganizing biodiversity data accessible through
GBIF.
• GBIF Colombia released a new version of its
portal following another round of improvements
in its usability. The changes include an enhanced
look and feel for the site, sortable tables and theuse of a GitHub repository, a software framework
simplifying collaborative development. Read thefull list of enhancements...

NEW TOOLS AND RESOURCES
Smartphone apps for plant identificationfrom images …
A France-based website has launched an iPhone
application enabling amateur botanists to upload
plant photos for identification by experts, andpublication as occurrence records through the GBIF
network. The images are sent to iHerbarium, whose
volunteer experts help identify the plant and send an
email with the information back to the user.
The images and related information go into acentral database, making future identifications

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easier. Validated data are published to GBIF throughthe Agoralogie society which promotes scientificcollaborations using the semantic web. The
iHerbarium app is available in French and English,
and the website also in Spanish and Portuguese. An
Android application is promised shortly.

… and for keys to identify insects andinvasive weeds
Users of Android mobile devices now have newtools to help identify insects and invasive plants inAustralia. A team at The University of Queensland has
developed a mobile version of the Lucid software,
allowing identification tools or keys to be deployed
as smartphone apps, initially for Android devices butwith iPhone/iPad versions to follow shortly.
Two Lucid keys have already been made available on
the Google Store – a free key to Insect Orders, and a
key to Environmental Weeds of Australia.
The insect key is designed to help advanced
secondary school students, undergraduates andothers interested in entomology to identify the mostcommon adult insects to Order level in Australia. The
second key includes over 10,000 images helping users
identify 1,020 plant species that are either significant
or emerging weeds in Australia. It should be usefulfor researchers and anyone involved in weed control.
While focused on Australia, the key is also an
excellent resource for users in other countries.

New Wiki site on thrips
An international group of taxonomists has launched
a new website giving information on nearly 6,000
insect species belonging to more than 800 generaof the Order Thysanoptera, also known as thrips,
thunderbugs or corn lice. ThripsWiki is supported byAustralian Department of Agriculture, Fisheries andForestry (DAFF), and builds on a checklist compiledin 2005 by Australia’s science agency CSIRO, withfunding support from GBIF, to check data from major
thrip collections in Frankfurt, London and Washington
DC.
Lichanothrips pastinus, type specimen from the Australian National
Insect Collection, CanberraAug 2011

SCIENCE AND POLICY
GBits Science Supplement
As usual, GBits is accompanied by a Science
Supplement featuring recent uses of GBIF-mediateddata. The latest issue highlights research suggestingthat invasive species shift their ecological ‘niche’ intheir new environments; and a special issue of thejournal Biodiversity Informatics focussing on demanddriven biodiversity data publication.

no 35 Jul 2013

The new centre is a $16m expansion of the original
Biodiversity Institute of Ontario, tripling the size ofthe former facility, and will house the secretariatof the International Barcode of Life (iBOL), a GBIF
Associate Participant. DNA barcoding allows scientists
to identify animal and plant species using short,standardized regions of genetic material.
Read full story…

NEW DATA

Download GBits Science Supplement...

Belgium

AROUND THE NETWORKThe Flemish government’s Research Institute for
Nature and Forest (INBO) has published a number ofdatasets related to human impacts on the region’srivers and efforts to restore riverine habitats. The newdata now available through GBIF include:

Call to mobilize biodiversity data from
sub-Saharan Africa
The Central African Biodiversity Information Network(CABIN) is calling for proposals for the mobilizationand online publication of biodiversity data from subSaharan Africa. The aim is to preserve data belonging
to institutions in the region, to improve technicalcapacity and to make the data visible throughnetworks such as GBIF. The data will be physically held
on a server located at the Royal Museum for Central
Africa in Belgium, with selected African scientists
retaining full remote access and control as owners
and administrators of the datasets.
The deadline for applications is 31 August 2013.
More details...

Grants awarded to digitize US
biodiversity collections
Eight projects in the United States will receive grants
under the latest phase of the Advancing Digitizationof Biodiversity Collections (ADBC) programme, fundedby the National Science Foundation (NSF). The awards
involve 65 institutions in 29 states and one territory.
The projects include a collaboration on fossil insect
data to help understand the diversification of species
and response to environmental change; a centralized
digital archive of vouchered animal communication
signals; and a consortium accessing 150 years ofspecimen data on algae to understand changes in themarine/aquatic environment.
Read full story….

New genomics centre in Canada to house
DNA barcoding project
The University of Guelph in Ontario, Canada, has
opened a new Centre for Biodiversity Genomics(CBG), focussed on discovering, identifying andcataloguing species using DNA barcoding technology.

• Over 1,100 records of glass eels from the riverYser, captured during their migration for a study
on the species’ distribution;• Juvenile and adult fish occurrences from samplingof contrasting habitats along the river Yser toevaluate a restoration programme in an area
degraded by human activities such as raising ofbanks and heavy shipping traffic;• Data from similar sampling of fish in the river Leie,to evaluate the impact of artificial banks;• 5,800 occurrence records of ground beetles(Carabidae) from the banks of the river Meuse.
The dataset contains information on 109 species
and comes from a monitoring study of theGrensmaas region, the stretch of the Meuse
bordering Belgium and Holland. The records areamong the data used in studies to measure theriverine habitat’s health.

Netherlands
The NGO Reptile, Amphibian and Fish Conservation
Netherlands has published historical data on
3,700 fish observations extracted from reports by
Dutch naturalists in the late nineteenth and early
20th centuries. They include records of fish in theZuiderzee reported in 1890, 1907 and 1921, and fromthe lower Rhine-Meuse delta reported between 1886
and 1896.
The Natural History Museum of Rotterdam has
published 68,000 records of molluscs from its
collection of snails and slugs living in marine, land
and freshwater environments. The museum has also
shared 94,500 records from its insect collection.

FranceThe Service du Patrimoine Naturel of the National
Museum of Natural History in Paris has publishedmore than 30,000 marine data records from the seas33

GBitsoff the French Mediterranean, Atlantic and English
Channel coastlines. They include:• An aerial survey of marine megafauna, including
records of ocean sunfish, dolphins, fin whales,
sperm whales, sharks, giant devil ray, long-finned
pilot whale, leatherback turtle and seabirds;• 190 observation records of sea horses andpipefish;• 8,700 records of seabed-dwelling organisms suchas starfish observed at marine stations; and• 5,100 records from a biodiversity inventory tohelp identify marine sites under the European
Union’s Natura 2000 network of protected areas.
The University of Strasbourg published 3,780 recordsof herbarium specimens from Wallis and Futuna, aFrench island territory in the South Pacific.

Germany
The Bavarian Natural History Collection (Staatliche
Naturwissenschaftliche Sammlungen Bayerns) has
published over 100,000 records, including:• more than 20,000 microorganism records fromthe Jena Microbial Resource Collection;• 8,000 records from the diatom collection of Franz
Josef Weinzierl, held at the Botanical museum in
Munich;• 48,400 records from the fungus collections at theState Museum of Natural History – Karlsruhe; and• 27,000 records of arthropods from the Bavarian
State Collection of Zoology.
A new publisher, the University of Greifswald has
published over half a million records of nearly
2,500 plant species from the Mecklenburg-Western
Pomerania state in northern Germany, based on a
floristic survey of eastern Germany. Members of the
public can contribute additional information on theflora of the region at http://www.flora-mv.de.

Ireland
The National Biodiversity Data Centre (NBDC), hostof the GBIF national node for Ireland, has published
350,000 records to the network, including:• 342,000 plant records collected from county
Wexford in southeast Ireland since the 18th
century, by the county recorder of the BotanicalSociety of the British Isles.
• 1,100 records of rare marine fish species, such as
the critically endangered European sea sturgeon(Acipenser sturio), taken in Irish waters by fishingvessels and sea anglers from 1786 to 2008.
• Data on breeding wading birds from surveys in1985 and 1996 of machair habitats, a type of lowlying grassy plain found on the northwest coast of
Ireland;• Records from a database under development
for caddisflies of Ireland, from a survey of newt
distribution in Ireland since 2010, records ofaquatic worms, and of freshwater fish in Irish
4 lakes.

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SwedenThe Swedish Museum of Natural History published
about 150,000 records from its insect andpaleontological collections. Observations from the
Malaise Trap Project, a national insect inventory, arealso among the published data. The project uses tentlike traps made from mosquito net fabric, devised
by Swedish entomologist René Malaise in the 1930s.
Such traps are standard equipment in insect surveys
around the world today.

United Kingdom
The UK National Biodiversity Network, host of the
GBIF national node, published 862,000 records fromcounty surveys. Over half of these are from Ecorecord,
an ecological database covering Birmingham and theBlack Country in the English Midlands. Other datasets
include:• freshwater fish, cetaceans, butterflies andmammals from Cheshire in the northwest of
England;• 15,100 records of insects from Derbyshire;• 7,800 records from a survey of invasive Himalayanbalsam in Bedfordshire and Luton; and• 95,000 records of moths from Sussex.

CanadaThe University of British Colombia has published
20,800 records of mammals, reptiles and amphibians
from its Cowan Tetrapod Collection. The collection
contains specimens dating back to the early 1900s,
including 7,000 bird eggs from 625 species. The
dataset is hosted by the VertNet network.

Colombia
Three institutions from Colombia have become newdata publishers in the GBIF network:• Oleoducto Bicentenario, an oil company set up to
operate a private pipeline, has published 2,000
records of epiphytes, plants such as orchids andbromeliads that use trees for support. The plants
were transferred to new locations during theconstruction of the pipeline between Araguaney
in Casanare department and Banadia in Arauca
department, in northern Colombia. This is thefirst of three phases in the construction of thepipeline, which will end in the port of Covenas.
• The environmental authority for the municipalityof Bucaramanga - Corporación Autónoma
Regional Para la Defensa de la Meseta de
Bucaramanga - has published 6,800 records
from its collection of 2,300 plant species in thedepartment of Santander.
• The non-governmental organization (NGO)Calidris, set up to study and conserve the aquaticbirds of Colombia, has published 1,700 recordsof 50 species of waterbirds. The dataset includes
observations between 2007 and 2009 in theAug 2011

Sanquianga national park and the Iscuandé
estuary, on Colombia’s Pacific coast, which holdsome of the largest known concentrations of
sea and shorebirds in the country. Calidris also
published records of 22 prey species found in
the diet of the brown booby (Sula leucogasteretesiaca) in the Gorgona national park between
June and December 2006. Information on therichness, composition and abundance of prey is
included.
Brown booby (Sula leucogaster) perched on a floating tree trunk. ©
Luis Alejandro Bernal Romero

no 35 Jul 2013

TRAINING AND
COLLABORATION
E-learning course on generating data
papers
GBIF Spain has developed an online Spanish-language
course on publishing data papers for scientists andprofessionals working on collections, as well as
administrators who compile biodiversity data forfurther sharing.
The course helps participants to author manuscripts
for peer review, based on descriptions of biodiversity
datasets (metadata), using the GBIF Integrated
Publishing Toolkit (IPT). Data papers offer scholarly
recognition for data publishers. The course is basedon material from the workshop on data paper
publication held in March in Madrid.
The course is self-guided and is free of charge.
All material is in Spanish. Registration is at http://
elearning.gbif.es/.

Online forum for biodiversity informationin Latin America and Spain
ZooKeys journal

An online forum for discussions on biodiversity
informatics has been started by the IberoAmerican
Infrastructure for Biodiversity Information (I3B), a
platform for collaboration among organizations in
Latin America and Spain.

The first study described a new species of burying
beetle, Nicrophorus efferens, from BougainvilleIsland in the Solomon Islands archipelago of the
Pacific Ocean. The authors from University of
Alaska Museum made the discovery using six beetle
specimens collected from the island in the 1960s and70s and held in a museum in Hawaii. These are now
type specimens (defining examples of a taxon) for the
new species, and the details of their collection dates
and locations are published through GBIF. Burying
beetles get their name from their habit of burying
the carcasses of small vertebrates such as birds androdents as a food source for their larvae.

New users may register online to use the forum.

Two research teams have published datasets
associated with taxonomic studies in ZooKeys journal,
shared with the GBIF network through software
installed by Pensoft, publishers of the journal.

Read a news story on the new species…
In a second study in ZooKeys, researchers from San
Diego State University reviewed the Acuclavellagenus of harvestmen, relatives of spiders often
known as daddy-long-legs. The authors collected
284 harvestmen specimens in 61 localities in Idaho,Montana and Washington states, and their analysis
identified three new species within the genus. Detailsof the specimens associated with the study, includingcollection locations and dates, are now accessible as adataset through the GBIF portal.

Georeferencing training in South Africa
The ‘train the trainers’ approach is helping to build
up expertise among professionals in South Africa on
georeferencing biodiversity records – so improving
the quality of data available for research and policy.
The South African National Biodiversity Institute(SANBI), which hosts the GBIF national node,
coordinated and supported a training course inJune for 17 participants from universities, researchcouncils, museums, mining companies and fromSANBI itself.
The trainers, from the KwaZulu Natal Museum,Eastern Cape Parks and Tourism Agency and theAgricultural Research Council, were themselves
trained in 2011 at a workshop run by experts from theMuseum of Vertebrate Zoology in Berkeley, California,
who have helped to develop the informatics tools andstandards used across the GBIF network.
The training helped participants to contribute moreaccurate descriptions of the location of biodiversity,

55GBitswhether at the stage of collecting data, managing
datasets or when publishing data.
This was the second workshop of its kind, with thefirst held at the Kwa-Zulu Natal Museum in November
2012.
Read the full story...

GBIF IN THE NEWSThe announcement of the 2013 GBIF Ebbe Nielsen
prize and Young Researcher Award winners wascovered in a number of newspapers and news
websites in Mexico, Portugal, the United States andDenmark. Coverage included:

Other coverage in this period included an article oninvasive species in Tanzania, on the news site The
Daily News. The Tanzanian Biodiversity Information
Facility (TanBIF) and GBIF are mentioned in the article.

UPCOMING EVENTS
Meetings and workshops
Biodiversity Informatics Horizons 2013
3-6 September 2013, Rome, Italy
More information…
2nd Biodiversity Knowledge Conference
24-26 September 2013, Berlin, Germany
More information…

For Ebbe Nielsen Prize winner Miguel Bastos Araújo:• the print edition of the Portuguese daily Jornal deNotícias• print edition of a major Portuguese weekly, Visão
• UEline – online bulletin of the University of Evora• Ciência Hoje, a news portal on science, technology
and entrepreneurship• Altinget, a Danish news portal on research andinnovation

20th meeting of the GBIF Governing Board, new GBIF
portal launch and Science Symposium
8-10 October 2013, Berlin, Germany
More information…

For GBIF Young Researchers Award winner Emma
Gómez Ruiz:• News website Periódico El Planeta• News website Mi Ambiente• AgriLife Today, bulletin of the Texas A&M
University• Reforma, a leading Mexican newspaper

5th International Barcode of Life Conference
27-31 October 2013, Kunming, China
Abstract deadline: 16 August 2013
More information…

GBIF was mentioned in several other online and print
media outlets in June and July. Among these were a
Comment article in the weekly science journal Natureentitled Agriculture: Feeding the future. Arguing theneed to mine biodiversity in seed banks to overcome
food shortages, the article describes GBIF as a good
example of an internationally accessible informatics
infrastructure which “has changed how biodiversity is
studied” – while noting that GBIF does not currently
handle the complex genomic data necessary for theefforts needed to ‘feed the future’.

GB20 Nodes training course: building stronger GBIF
Nodes
4-5 October 2013, Berlin, Germany
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 Ø
Denmark

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

http://www.gbif.org/
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17th Meeting of the CBD Subsidiary Body on
Scientific, Technical and Technological Advice (SBSTTA)
14-18 October 2013, Montreal, Canada
More information…

Training events

GBits archive: http://www.gbif.org/communications/
resources/newsletters/