GBits

no. 43 Apr 2015

free and open access to biodiversity data

GBIF and EU to improvebiodiversity information fordeveloping countries

DATA PUBLISHING � � � � � � � � � � � 2
New opportunity for publication of
species sampling and monitoring data
New GBIF task force to speed up accessto natural history collection data
Software release supports consistent
DOI-based citation
Norwegian data increase by 25%

GBIF COMMUNITY � � � � � � � � � � � � � 3
New GBIF Participants
New publications to guide sustainable
mountain development in Africa
GBIO report now available in Japanese
New citizen science records onAustralian data portal
Specimen digitization workshop. Photo by Jean Ganglo.

The European Union (EU) and GBIF have launched a fouryear €3.9 million project aimed at increasing the amountof biodiversity information available for developing
countries.
GBIF’s Biodiversity Information for Development (BID)
will focus on enhancing capacity and mobilizing datafrom countries in Africa, the Caribbean and the Pacific.
By gathering information relevant for policymakers,
BID will help those countries to meet key policy needs
and commitments under intergovernmental processes
like the Convention on Biological Diversity (CBD) andthe Intergovernmental Platform on Biodiversity andEcosystem Services (IPBES). BID will also help the
European Union fulfil the commitments made to avert
global biodiversity loss.

Portal of the German national
biodiversity data infrastructure
revamped

NEW DATA � � � � � � � � � � � � � � � � � � � � 4
GBIF DATA IN USE � � � � � � � � � � � � � 5
TRAINING� � � � � � � � � � � � � � � � � � � � 8
Data publishing training organized in
North America
Hackathon targets preparing national
checklists
Course material from Biodiversity
Informatics week in Brazil available
online
GBIF Portugal organizes seminar series

EVENTS � � � � � � � � � � � � � � � � � � � � � � 9read more
Information page on GBIF.org

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

GBitsDATA PUBLISHING
New opportunity for publication of
species sampling and monitoring data
Biodiversity Information Standards (TDWG), theinternational body responsible for maintaining
standards for the exchange of biological data,
has ratified changes that improve support formobilization and access of sample-based species
data through the GBIF network.
By adding to the rich set of terms already available
in the Darwin Core (DwC) standard, this ratification
will help GBIF-mediated data move beyond“presence only” data and support the discovery
and application of richer, more quantitative
information used in other areas of scientificdiscovery and research, particularly ecologicalmonitoring and assessment.
In addition to bringing in new datasets, thesechanges could also improve the quality and utilityof many datasets already published through GBIF,
which derive from the more complex sources
required to understand how species populations
change across space and time.

consistent, traceable attribution of GBIF-mediateddata and downloads, streamlines how publishers
define appropriate uses of their data, and improves
data quality control.
read moreNews release

Norwegian data increase by 25%
The Norwegian Biodiversity Information Centre(NBIC) added 3.5 million observation records to theNorwegian Species Observation Service dataset in
December, bringing the total number of records inthe dataset to nearly 11 million.
The dataset’s dynamic growth is due in largepart to Norway’s Artsobservasjoner portal, which
gathers observations from 9,000 volunteers, whoreport an average of 5,000 observations eachday. Artsobservasjoner currently holds 12 million
records on over 14,000 species, along with morethan a quarter million images. These data feed
into the Species Map Service, which shares morethan 19 million species occurrence records related
to over 31,000 species, provided by 34 Norwegiansource institutions.

read moreNews release

New GBIF task force to speed up
access to natural history collectiondata
A team of international experts convened by GBIF
intends to help accelerate the discovery of andaccess to information about the world’s undigitized
specimen collections.
The task force on accelerating the discovery of
bio-collections data will start by defining theessential information needed about various typesof collections. This ‘metadata’ will describe thecontents of each collection and help data holders toassess and prioritize their digitization activities.
read moreNews release

Software release supports consistent
DOI-based citation
The GBIF Secretariat has published version 2.2 of
its Integrated Publishing Toolkit (IPT), a free opensource software tool for publishing and sharing
biodiversity data. The new version supports22

Musk ox (Ovibos moschatus). Image by Bernt Kåre Knutsen publishedon Artsobservasjoner.no.

National and regional agencies, county governors,
municipalities, private companies and scientificinstitutions use these data extensively.
NBIC expects a continued steady increase in
species reporting and publishing through GBIF.org
this year.
To learn more, contact Dag Endresen or Nils Valland
at NBIC.
read more
Behind the scenes: creating and operating
the Species Observations database

Aug 2011

GBIF COMMUNITYNew GBIF Participants
The southeast African country of Malawi andSwiss non-profit organization Plazi are the newest
Associate Participants in GBIF, while Togo has
moved its status to Voting Participant.

no. 43 Apr 2015

The Japanese version includes new material aimed
at helping users, including a commentary on open
data and semantic web, and a glossary.
DOWNLOAD REPORTNew citizen science records onAustralian data portal“Joining GBIF will help Malawi gathering
biodiversity data relevant for policy makers,”
said Lyson Kampira, manager of the new GBIF
node at the National Commission for Scienceand Technology, noting its relevance for meetinginternational commitments for the CBD and IPBES.
Plazi supports linked open-access biodiversity
data drawn from taxonomic literature, and Donat
Agosti, president of Plazi, acknowledged “theshared efforts of both organizations to provide
critically needed access to vast stores of data andknowledge about species found in biodiversity
literature.”
Togo’s move from Associate to Voting Participant
gives the country a direct role in GBIF’s governance.
The West African nation has participated in GBIF’s
capacity enhancement programme, mobilizing
specimen records from the country’s herbarium andpublishing checklists related to leguminous plants,
algae and West African mushrooms.

New publications to guide sustainable
mountain development in Africa
Albertine Rift Conservation Society, a GBIF
Associate Participant, UNEP and partners havereleased two landmark publications—the African
Mountains Atlas and the African Mountains
Status Report—to guide sustainable mountain
development in the continent. Both publications
will support planners and decision makers in Africa.
read more

Anthracophyllum archer, from ALA’s Fungi map

Fungimap, one of the largest citizen science groups
in Australia, has been around for 20 years, but
recent support from the Atlas of Living Australia(ALA), GBIF’s national node, has helped deliver its
data to a wider audience.
read more
Blog post
By providing a GPS-enabled smartphone app, ALA
also enabled quick reporting of sightings for the
National Koala Count. These data complement
existing records, and a full report on the 2014
results is available.
read more
Blog post

Portal of the German national
GBIO report now available in Japanese biodiversity data infrastructure
revamped
News release

JBIF, the GBIF node in Japan, released a Japanesetranslation of the Global Biodiversity Informatics
Outlook (GBIO) at a December workshop in Tokyo.
By focusing effort and investment in biodiversity
informatics, the GBIO report provides a frameworkfor harnessing the power of technology and an open
data culture for the benefit of biodiversity.

GFBio, the German Federation for Biological Data,
has been relaunched with new tools and services,
including new search features and in-depth
information about the data life cycle. Nineteen
partner institutions, including national node hosts- the Botanic Garden and Botanical Museum BerlinDahlem (BGBM), Museum für Naturkunde (MfN),
Senckenberg Gesellschaft für Naturforschung,the Bavarian Natural History Collections and the33GBits
Zoological Research Museum Alexander Koenig help implement the work of GFBio.
read moreNews release

Ornitológica del Plata, the oldest environmentalorganization in South America. The data represent
more than 40 years’ worth of observations by
Argentinian ornithologist Tito Narosky, author of
Birds of Argentina and Uruguay, a Field Guide.

NEW DATA

Belgium

New species data on GBIF.org

46 occurrences of forage plants collected in the
Democratic Republic of Congo by the Université
Pédagogique Nationale, Kinshasa were publishedby the Royal Museum for Central Africa in Belgium.

An ongoing collaboration with Pensoft Publishers
to unlock and preserve the value of ‘small data’has led to a steady stream of new datasets fromresearch related to the description of new species
and species distributions published in the peerreviewed Biodiversity Data Journal.
Notable examples include:

Benin
GBIF Benin has published three new datasets fromrecent censuses:• More than 18,000 records gathered in 2014 for aplanned national atlas of the animals of Benin.
• A national forest census including more than
40,000 records• 3,161 plant occurrences in the Agrimey forest
reserve in southern Benin.

CanadaHolotype of Neoniphon pencei, Rarotonga, Cook Islands Photo by
Richard Pyle and Brian Greene• Neoniphon pencei, a new species of ray-finned
fish described from Rarotonga, Cook islands• Margaromantis piza, a second species of theneotropical mantid genus from Brazil• Vigna yadavii, a new species of cow pea
identified in the Western Ghats of India• Land snails in the Srebarna Nature Reserve in
Bulgaria• Distribution of the Laotian rock rat (Laonastes
aenigmamus), the only surviving member of theotherwise extinct rodent family• Distribution of an endemic leaf-nosed bat(Hipposideros durgadasi Khajuria) from south
India.

Argentina
The Ministerio de Ciencia, Tecnología e Innovación
Productiva (Ministry of Science, Technology andProductive Innovation) has published 10,919
observations in a collection of 54 new bird family
datasets from Aves Argentina / Asociación44Cretaceous dinosaurs from Alberta and Jurassic
ichthyosaurs from Saskatchewan are among thespecimens published by the Royal Ontario Museumfrom their collection of vertebrate fossils. The
24,600 records published represent one-third of
the century-old collection of more than 72,000
catalogued specimens.

Colombia
The Alexander von Humboldt institute, host of the
GBIF national node, has published data on plants,
soil fauna, amphibians and birds in the highaltitude páramos ecosystems of Los Nevados andChili-Barragán in the Colombian Andes.
The Institute also published bird data from a 2006
study in the Caldas department, which includes
records of two endangered species – the yellowheaded brush finch (Atlapetes flaviceps) and Stiles’
tapaculo (Scytalopus stilesi).
Colombia’s universities have published new several
datasets, including:• the insect collection of the Universidad
Tecnológica del Chocó• the fish collection of the Universidad Industrial
de Santander• aquatic plants of the Orinoquía region from the
Universidad de los AndesAug 2011• the fish collection of the Universidad Católica deOriente.
Other new Colombian datasets include rainforest
vegetation plots from REDD+ (Reduced Emissions
from Deforestation and Forest Degradation)
projects in• Bahía Málaga, Valle del Cauca• Rio Cajambre, Valle del Cauca• ChocóGermany
The Botanic Garden and Botanical Museum BerlinDahlem has published a dataset with more than
15,000 photographs of type specimens collected
in Central and South America between 1778 and
1930. The images are the work of botanist J.Francis
Macbride, whose photographs of these tropical
American plants in European herbaria became evenmore valuable when parts of the collections weredestroyed during World War II.

no. 43 Apr 2015

PortugalCitizen scientists’ observations of invasive plants
in Portugal are now available from invasoras.pt,
a combined web platform and phone application
developed at the University of Coimbra’s Centre for
Functional Ecology.
The National Museum of Natural History and
Science at the University of Lisbon has publishedmore than 6,000 herbarium records of Angolan
plant specimens dating back to the mid-nineteenth
century.

Spain
The VIT herbarium at the Museum of Natural
Sciences of Alava, Spain has published records formore than 85,000 plant specimens, mostly from
Spain.

GBIF DATA IN USE
The Secretariat maintains a programme to monitor
use of GBIF-mediated data in scientific literature.
The following peer-reviewed articles represent somerecent highlights.
Bradley BA, Early R & Sorte CJB (2015) Space toinvade? Comparative range infilling and potential
range of invasive and native plants. Global Ecology
and Biogeography.

Image of type specimen of Oreopanax trollii Harms from the collectionof BGBM’s historical photographs.

India
The Wildlife Institute of India, host of the GBIF
national node, has published 31,936 recordsof recent bird observations from the Keoladeo
National Park in north India. Previously known as
the Bharatpur bird sanctuary, the park is listed as a
UNESCO World Heritage Site due to its significanceas wintering grounds for migratory birds.

Japan
The National Institute of Genetics has publishedoccurrence data for migratory shorebirds captured
in the marshes and lakes of Hokkaido as part ofa study of avian infections of West Nile virus andhaematozoa.

Testing the notion that species distribution models
predict disproportionately smaller potential ranges
for non-natives than natives, researchers compared
the distributions of 13,575 native, endemic,alien and invasive plants in the United States
to determine how these groups’ different range
attributes might influence ecological forecasting.
Describing GBIF as “the only source that could
consistently provide distributional data for all of
our target species at a global scale”, the study
concluded that invasives had not achieved the
expected degree of range infilling, suggesting that“plants introduced to the US still have plenty ofspace to invade”.
Campbell J (2014) Access to scientific data in the
21st century: rationale and illustrative usage rights
review. Data Science Journal.
A researcher into information policy and accessdescribes the need for establishing clearer
definitions of ‘open access’ while outlining how
freely available scientific data can encourageboth validation of research results and economic
development.
55GBitsCandela L, Castelli D, Manghi P & Tani A (2015) Datajournals: A survey. Journal of the Association for
Information Science and Technology.
Authors cite the GBIF’s Integrated Publishing
Toolkit as one tool that provides direct support
for describing and authoring peer-reviewed
datasets, which in turn increase the discoverability,
availability, and reuse of data by others.
Elmendorf SC, Henry GHR, Hollister RD, Fosaa AM,
Gould WA et al. (2014) Experiment, monitoring,and gradient methods used to infer climate change
effects on plant communities yield consistentpatterns.
To assess and address potential inconsistencies
in three common methods for modelling potential
climate impacts, a broad international team used
GBIF-mediated data from plant communities
in arctic and alpine North America and Europe
to analyse predicted changes in community
composition. Results from in situ experimental
warming and monitoring approaches yieldconsistent estimates of the communities’
magnitude of response to contemporary climate
warming, while inferences based on present-day
patterns of ecological systems tend to overestimatethem.

.......

offer new options for sawfish conservation in the
Atlantic and highlight the importance of historicalanalyses for reconstructing ecosystem baselines
and setting recovery targets.
Ficetola GF, Rondinini C, Bonardi A, Basiero D& Padoa-Schioppa E (2015) Habitat availability
for amphibians and extinction threat: a global
analysis. Diversity and Distributions. Journal of
Biogeography.
Despite the threats of habitat loss and degradation
detailed by the IUCN Red List over the past decade,quantitative measures of habitat exist for only asmall subset of amphibian species. Using morethan 200,000 GBIF-mediated records along withother data, researchers produced models for
5,363 amphibians (84% of the species evaluatedby the IUCN’s Global Amphibian Assessment) andfound that models can accurately predict finescale distribution of many species, suggesting
their usefulness as a complement to expert-led
conservation assessments.
Fuller P & Neilson ME (2015) The U.S. Geological
Survey’s Nonindigenous Aquatic Species Database:over thirty years of tracking introduced aquatic
species in the United States (and counting).
Management of Biological Invasions.
In describing the capabilities, functionality,and 40-year history of this U.S. database, theauthors outline how it harnesses the wealth ofother sources of biodiversity and biogeographic
observation data, including more than 12,000
records harvested via the GBIF.org API.

Sawfish (Pristis pectinata). Photo by David Iliff.

Ferretti F, Verd GM, Seret B, Šprem JS & Micheli F(2015) Falling through the cracks: the fading historyof a large iconic predator. Fish and Fisheries.
Sawfishes are among the world’s most endangered
marine vertebrates. Human impacts havecontributed to their extinction from many coastal
waters, and debates about their past presence
and possible extinction in the Mediterranean
have carried on for decades. This research teamreconstructed the history of the occurrence of two
sawfish species in the western Mediterranean
between 1576 and 1959, using records accessed
through GBIF among other sources. By suggestingthat both species went extinct in the Mediterranean
in the 1960s or 70s, the results challenge current
assumptions on sawfish ecology and biogeography,
6

6

Lionfish (Pterois miles), an invasive species along the east coast of
the United States. Photo by Lindley Ashline.

Aug 2011

no. 43 Apr 2015

García-Roselló E, Guisande C, Manjarrés-Hernández
A, Gonzálex-Dacosta J, Heine J et al. (2014) Can
we derive macroecological patterns from primary
Global Biodiversity Information Facility data? Global
Ecology and Biogeography.
To understand the impact of data samplingbiases and quality concerns in global-scale
macroecological models, this team used allavailable GBIF-mediated data for fish species
from marine-only orders to compare four common
procedures. Provided that researchers clean theoriginal data, correct for autocorrelation andaccounting for obvious underestimations in species
richness, the findings suggest that improving
data quantity and quality may matter more thansophisticated mathematical models in predicting
the distributions.
Lira-Noriega A & Soberón J (2014) The
relationship among biodiversity, governance,
wealth, and scientific capacity at a country level:
Disaggregation and prioritization. AMBIO.
The authors examine the relationships between
biodiversity richness, wealth and institutional
capacity in more than 200 countries and territories,
using the number of records mobilized through
GBIF as part of an index of scientific capacity.
Such relationships are not simple, and patternsof wealth and capacity show a more complicatedpattern that cuts against conventional wisdom. The
paper concludes by encouraging collaborations toimprove access to primary biodiversity data, both
digitized and not, that are not yet available foranalysis, science and policy.
Mathew C, Güntsch A, Obst M, Vicario S, Haines
R et al. (2014) A semi-automated workflow forbiodiversity data retrieval, cleaning, and quality
control. PNAS.
To address the time-consuming and complex
process of compiling and preparing data for
analyses and prediction of species distributions,the researchers describe the design andimplementation of a Taverna-based data refinement
workflow for retrieving, cleaning and selecting
taxonomic data from sources including GBIF.org and
the GBIF API.

Pristimantis cruentus. Photo by Brian Gratwicke.

Mendoza ÁM, Ospina OE, Cárdenas-Henao H& García-R JC (2015) A likelihood inference ofhistorical biogeography in the world’s mostdiverse terrestrial vertebrate genus: Diversificationof direct-developing frogs (Craugastoridae:
Pristimantis) across the Neotropics. MolecularPhylogenetics and Evolution.
This analysis of new and published DNA
sequencing data helps improve understanding of
how the geological complexity of the Andes may
have contributed to the astounding diversity of
Pristimantis, a frog genus composed of more than
420 species. Combining GBIF-mediated data withinformation from the Global Amphibian Assessment
and recent publications that describe new records
and range extensions, researchers reconstructed
ancestral range maps suggesting that the
paleogeological changes in the northwestern Andes
promoted diversification and dispersion of thegenus across a wide swathe of Central and SouthAmerica.
Owen CL, Bracken-Grissom H, Stern D & Crandall
KA (2015) A synthetic phylogeny of freshwater
crayfish: insights for conservation. PhilosophicalTransactions B.
Drawing upon GBIF-mediated data as well as othersources, the authors describe their use of The Open
Tree of Life, a user-curated taxonomic project, tocreate a synthesis evolutionary tree for freshwater
crayfish. Their conclusions present the threat
distribution across species, an estimated molecularphylogeny, and analyses identifying freshwater
crayfish species that are high-priority candidates
for conservation efforts.

77

GBitsvan Andel TR, Croft S, van Loon EE, Quiroz D,
Towns AM & Raes N (2014) Prioritizing West
African medicinal plants for conservation andsustainable extraction studies based on market
surveys and species distribution models.
Biological Conservation.
Wild-harvested medicinal plants are an importantsource of health and trade for people in subSaharan Africa. By combining quantitative surveysof herbal markets in Ghana and Benin with thefirst detailed distribution maps for 12 commerciallyextracted medicinal plants (which draw upon GBIFmediated data), this study assess the potential
vulnerability of species to overharvesting withthe goal of safeguarding important provisioning
services of West African ecosystems.

Paknia O, Rajaei Sh. H & Koch A (2015) Lack ofwell-maintained natural history collections andtaxonomists in megadiverse developing countries
hampers global biodiversity exploration. Organisms
Diversity & Evolution.
Described as the first critical assessment of
current conditions of institutional infrastructure
in biologically megadiverse developing countries,
this research highlights a shortage of trained
taxonomists and the lack of well-maintainedcollection infrastructure as the main bottlenecks
for biodiversity exploration. Citing GBIF.org’shigh proportion of observational data and small
proportion of records with photographs for voucher
specimens, the authors call for an expansion ofdigitization projects aimed at covering all voucher
specimens in natural history collections worldwide.
Wisz MS, Broennimann O, Grønkjær P, Møller PR,
Olsen SM et al. (2015) Arctic warming will promote
Atlantic–Pacific fish interchange. Nature Climate
Change.
With the Arctic warming rapidly, the long-term
barrier separating the marine organisms of theNorth Atlantic and the North Pacific is becoming
less formidable. Using data gathered from GBIF
and the Ocean Biogeographic information System,
researchers forecast the potential northward
progression of 515 fish species due to climatechange, finding that as many as 41 fish species
could enter the Pacific and 44 species could enter
the Atlantic by 2100.

TRAINING
Data publishing training organized in
North America
Seventy-four data and collection managers,
taxonomists, curators and researchers gathered in
Ottawa, Canada, and Gainesville, Florida, on 13-14
January 2015 for a training event on publishing andsharing biodiversity data using the GBIF Integrated
Publishing Toolkit (IPT).
Sun drying of Piper guineense fruits at Bode Market in Ibadan,
Nigeria. Photo by the International Institute of Tropical Agriculture.

Co-organized by iDigBio, VertNET, Canadensys,
Agriculture and Agri-food Canada, the Canadiannode CBIF, USGS-BISON and GBIF, the event
connected participants via the Internet as they
published test datasets. A preliminary webinar on 7
January focused on installing IPT.
read more
iDigBio website

88

Aug 2011

Hackathon targets preparing national
checklists
A training hackathon in the Netherlands brought
together staff from GBIF’s European nodes togenerate national species checklists using GBIFmediated data. Participants received training
in cross-mapping tools and in the creation of
workflows needed for checklist creation.
The event was one of five GBIF capacity
enhancement grant recipients for 2014, andpresentations are available here.

Course material from Biodiversity
Informatics week in Brazil available
onlineno. 43 Apr 2015

data, and participants expressed interest in data
papers and the way in which they provide credit fordata publishers.
read moreNews release

EVENTSICLEI World Congress 2015
8 - 12 April 2015, Seoul, Republic of Korea
7th European Nodes Meeting
5 - 7 May 2015, Paris, France
Africa Rising: Mobilising Biodiversity Data for
Sustainable Development
19-22 May 2015, Cape Town, South Africa

The National Laboratory for Scientific Computingin Brazil (Laboratório Nacional de ComputaçãoCientífica, or LNCC), host of GBIF’s national node,organized a full week of biodiversity informatics
courses led by international experts on data
publishing, data quality, niche modelling anddata visualization as part of its 2015 summer
programme.
Course materials are available from SiBBr.

GBIF Portugal organizes seminarseriesA series of ‘information days’ organized by GBIF
Portugal in six cities in the country brought in 159
participants from 26 different institutions.
The events introduced available data resources,
software and protocols to representatives ofuniversities, research institutions, the national
Institute for Nature Conservation and Forests –ICNF, regional and local administrations, privatecompanies, NGOs and aquariums. The seminars
also included hands-on sessions about using the

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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