GBits

no. 29 July 2012SCIENCE AND POLICY � � � � � � 2free and open access to biodiversity data

Conference targets
priorities for biodiversity‘intelligence’A landmark conference has agreed key priorities forharnessing the power of information technologies andsocial networks to understand better the workings of lifeon Earth.
The Global Biodiversity Informatics Conference (GBIC),
gathering some 100 experts from around the world from
2-4 July in Copenhagen, Denmark, identified critical areasin which greater investment and better coordination could
give society much better, innovative tools to monitor andmanage biological resources.
The overall aim is to build global collaboration on
biodiversity observation, uniting many partners andinitiatives, capable of detecting and enabling responses toshort-term changes and long-term trends in biodiversity
and ecosystems.
The major output of the conference will be a Global
Biodiversity Informatics Outlook (GBIO), setting out
priorities for the next 5-10 years in order to guide funding
agencies and broaden the evidence base for policies toconserve and sustainably use biodiversity. A draft of the
document will be circulated for comment throughout
the GBIF network and wider biodiversity informatics
community in early September.

DATA PUBLISHING� � � � � � � � � � 2
New GBIF reference guide for verifying zoological
names
OpenUp! project halfway to heritage access target

NEW DATA� � � � � � � � � � � � � � � � � � 2
GBIF COMMUNITY � � � � � � � � � � 4
Regional nodes meetingsThree GBIF mentoring projects selected forfunding in 2012
Translations available for key documents

AROUND THE NETWORK� � � � 6South African citizen science portal launched atforum
Canadensys explorer launched
Public invited to contribute to atlas of Irish
mammals
GBIF showcased at public science event inGermany

INFORMATICS � � � � � � � � � � � � � � 6
Task group to develop standard for species
descriptions
New tool for analysing datasets published through
GBIF
Darwin Core Archives now just a click away with
BioCASe 3.2

OPPORTUNITIES� � � � � � � � � � � � 7
i4Life Call for Pilot Projects – Building content for
the Catalogue of LifeUPCOMING EVENTS � � � � � � � � 7

A concise meeting report for GBIC is available here alongwith other key documents including formal presentations
and introductory comments by the Executive Secretary of
the Convention on Biological Diversity (CBD), Braulio Dias.

3rd European Congress of Conservation Biology(ECCB 2012)

GBIC was hosted by GBIF and the University of
Copenhagen, and organized in conjunction with
CReATIVE-B (Lifewatch), the Encyclopedia of Life, theConsortium for the Barcode of Life and the Natural History
Museum, London.

19th meeting of the GBIF Governing Board (GB19)

IUCN World Congress 2012
14th Annual BIOECON Conference

Biodiversity Technologies Symposium

Read more…

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

GBitsSCIENCE AND POLICY
A further 30 scientific research papers making use ofdata accessed through GBIF were identified during
June and July, bringing the total published so far
in 2012 to 119. The research includes papers on
predicting the relative abundance of species based on
occurrence data; on the factors influencing whether
alien species will survive successfully in their new
environment; and on differences between the likely
response of species on land and in the oceans toclimate change.
As usual, these papers are detailed in our GBits
Science Supplement, available online at http://www.
gbif.org/communications/resources/newsletters/.

DATA PUBLISHINGNew GBIF reference guide for verifying
zoological names
A new guide published by GBIF provides detailed
advice for those working with zoological names indigital environments.
The publication, Guidelines for the Captureand Management of Digital Zoological Names
Information, aims to promote consistency in thespelling and formats used for animal species
and genera, to avoid costly and time-consuming
subsequent efforts to link datasets referring to thesame species.
The advice provided in the manual is based on theInternational Code of Zoological Nomenclature(ICZN) and experience gathered over the years
by AnimalBase, a project set up in 2004 by the
University of Göttingen in Germany to digitize earlyzoological literature. It complements the substantial
documentation already made available by ICZN on
the issue of taxonomic names.

OpenUp! project halfway to heritage
access target
The EU-funded OpenUp! project has made more thanhalf a million photographs, videos, sound recordings,
drawings and other multimedia objects from leading
European natural history collections freely available
via the Europeana digital library and museum.
Led by the Freie Universität, Berlin, OpenUp! is a
consortium of 23 scientific institutions based in 12
European countries, including the GBIF Secretariat in
Copenhagen. The aim is to open up the great wealthof heritage contained in Europe’s natural history
museums and botanical gardens, with a target ofproviding at least 1.1 million objects to Europeana by
2014. Europeana currently provides access to over 23
2

2

Example of natural history objects published to Europeana:
Herbarium specimen, Common Cornflower (Centaurea cyanus L.) of
the Willing Collection, BGBM Berlin.

million books, paintings, films, museum objects, andarchival records from more than 2200 institutions in
33 countries.

NEW DATA
Following the latest update of the GBIF data index,
more than 377 million occurrence records wereaccessible through the data portal at the end of July,
including 329 million with geographical coordinates.
More than 10,000 biodiversity datasets have beenregistered by 419 data publishers.
A selection of new data coming into the GBIF network
during June and July is shown below.

Ghana
The Ghana Biodiversity Information Facility(GhaBIF) has published its first dataset, following amentoring project with NLBIF, the GBIF node in the
Netherlands. The dataset includes 85,000 records ofmore than 10,000 plant species from the Universityof Ghana’s herbarium located in the capital, Accra.

Aug 2011

The herbarium has one of the largest collections inWest Africa and has specimens from other countries
in the region. The data are published using NLBIF’s
Integrated Publishing Toolkit (IPT). (http://data.gbif.
org/datasets/resource/14195)

DenmarkPensoft Publishers’ open-access online journal
ZooKeys has published occurrence records for nearly
200 specimens of velvet spiders examined for ataxonomic study published in May. The article, Thevelvet spiders: an atlas of the Eresidae (Arachnida,
Araneae) reported a comprehensive analysis of thelineage of the Erisidae family, comprising nearly
100 species of spiders occurring mainly in Africa,
Europe and Asia and including some with spectacularcolouring such as the Ladybird Spider (see photo).

A male Ladybird Spider (Eresus kollari) found in the Czech Republic. 
Photo: Pavel Krásenský.

Jeremy Miller of Naturalis Biodiversity Center in the
Netherlands carried out the work with colleagues
from the United States, Denmark and the Czech
Republic, using electron microscopy and DNA
sequencing to analyse the phylogeny or relatedness
between the species. Records of the specimens
with their original collection locations, mainly
from Southern Africa and Europe, were published
to GBIF through the Integrated Publishing Toolkit(IPT) operated by Pensoft Publishers, and they are
hosted by Denmark. (http://data.gbif.org/datasets/
resource/14165)

United Kingdom
The University Museum of Zoology, Cambridge has
published more than 65,000 specimen records fromits collections, designated as being of outstanding
historical and international importance. Much of themuseum’s material was gathered during collecting
expeditions in the 19th century which provided
the first documentation of fauna in many parts of
the world. The collections therefore offer essential
baseline data against which to assess the current
distribution and status of species.
The Cambridge collections include individual
specimens of exceptional historical significance,

no 29 July 2012

including fine examples of the Dodo and Great Auk,skins of the extinct Tasmanian Wolf and many ofDarwin’s specimens, some of which were collectedfrom his voyage on the Beagle, and from his time
studying at the University of Cambridge. Morerecent additions to the collections include fossilsof the earliest land vertebrates, molluscs from the
excavation of the Channel Tunnel, which document
climatic change in Europe over the past 10,000
years, and a rich variety of invertebrate fauna fromthe Seychelles. (http://data.gbif.org/datasets/
resource/14193)

Germany
Users of the GBIF portal and web services now haveaccess to another historically important dataset
from the herpetological collection of the Staatliches
Museum für Naturkunde Stuttgart. The museum has
published over 7,000 records from the collection,
which dates back more than 200 years and includes
specimens contributed by leading 19th century
collectors such as Baron Carl Ferdinand von Ludwig,
Duke Paul Wilhelm von Württemberg, Baron F. vonMüller and August Kappler. The collection includes
some 20,000 reptile and amphibian specimens fromall over the world, with tortoises, crocodiles andneotropical amphibians forming an important partof the museum’s holdings. (http://data.gbif.org/
datasets/resource/14192)
The Senckenberg Museum für Naturkunde Görlitz
has published over 68,000 records from Edaphobase,a database on soil organisms such as earthworms,
threadworms, beetle mites, centipedes andothers. The information is based on more than 50
years of research. (http://data.gbif.org/datasets/
resource/14157)

Switzerland
The Global Mountain Biodiversity Assessment, a
network of the international research programme
DIVERSITAS, has published 163,000 records from its
Himalayan uplands plant database, which describes
plant species related to the Tibetan Plateau in Central
Asia. Data have been collected for over 50 years, in
13 countries. Over 2,200 collectors from all over theworld have contributed to this dataset and nearly all
the records are georeferenced. (http://data.gbif.org/
datasets/resource/14158)
The Mountain Invasion Research Network has
published over 3,700 observation records of nonnative plant species in some of the mountain areasof Australia, Chile, Spain and the United States.
Plants recorded include field pennycress, orchard
grass, chicory, Kentucky bluegrass and prickly lettuce.
(http://data.gbif.org/datasets/resource/14164)
The Centre Suisse de Cartographie de la Faune
has published over a million records of butterflies,33

GBitsdragonflies and orthoptera – grasshoppers, crickets
and locusts – from 1835 onwards. (http://data.
gbif.org/datasets/resource/14168, http://data.gbif.
org/datasets/resource/14169, http://data.gbif.org/
datasets/resource/14170)
Biodiversitätsmonitoring Schweiz, a programme of
the federal government, has published 26,700 birdobservation records from common breeding species
in the area. These include birds such as the Eurasianbullfinch, Eurasian collared dove, Mistle thrush
and the Blue tit. (http://data.gbif.org/datasets/
resource/14166)FranceUnited States

The United States Geological Survey (USGS) has
published over 100,000 records from its databaseof nonindigenous and introduced aquatic species.
The database, with records from virtually theentire country, was set up as a central repository
for accounts of introduced aquatic species, foruse by biologists, official agencies and the generalpublic. The records include species exotic to North
America, such as the Asian carp and zebra mussel,and fish species which have been transplanted from
native watersheds on the continent into non-native
watersheds, such as the bluegill and the largemouthbass. (http://data.gbif.org/datasets/resource/14300).

The Musée George Sand et de la Vallée Noire has
published 2,500 records of more than 1,300 species
from its collection of mounted bird specimens started
by Jean François Emmanuel Baillon, a naturalist
from northern France, during the 18th century. The
collection includes more than 60 specimens datingfrom before 1800, and nine examples of species orsubspecies that have gone extinct. (http://data.gbif.
org/datasets/resource/14302)

GBIF COMMUNITY

The Netherlands

The fourth meeting of the Asian nodes was organizedin Taipei by TaiBIF (GBIF Chinese Taipei), from 28 to
30 June. It involved 11 participants from five country
nodes (India, Japan, Korea, Pakistan and Philippines)
and three other Associate Participants (ACB, Chinese
Taipei and ICIMOD). Highlights included:

The Natural History Museum Maastricht has
published 22,240 records of plants from its
herbarium. (http://data.gbif.org/datasets/
resource/14173)

Belgium
The Research Institute for Nature and Forest (INBO)
has published over 72,000 records of ladybirds fromits Belgian Coccinellidae dataset. About 15% are frommuseum collections and literature data. The rest
are observation records provided by more than 500
volunteers. The records cover about 85% of Belgium.
(http://data.gbif.org/datasets/resource/14177)

CanadaThe herbarium of the University of British Columbia
has published 70,000 records of algae, including morethan 5,000 species collected between the 1950s
and 1980s, all along the Pacific coast from central
California to Alaska and the Aleutian Islands. (http://
data.gbif.org/datasets/resource/14174)
The Jardin Botanique de Montréal has published morethan 24,000 data records of living plant specimensfrom its collections, comprising almost 16,000
species. The garden is ranked as one of the largest of
its kind in the world. (http://data.gbif.org/datasets/
resource/14163)
Both of these datasets were published using theCanadensys data repository (see Around the Network,
p 6).
4

4

Regional nodes meetings
GBIF nodes in Asia, Africa and North America met inJune and July to enable collaboration at the regional
level and made progress on their regional strategicplans.

• Agreement on the major components of aregional action plan for Asia, recognizing thelimited amount of openly accessible biodiversity
data in the region. The plan foresees twocollaborative scientific initiatives, a content
and data mobilization strategy for the region,and strengthening biodiversity information andengagement. The two collaborative projects
will be on national species checklists, including
invasive, Red List, endemic species and migratory
birds for comparative study; and on updating
databases to assess the risk of fish biodiversity
loss in Asia.
A workshop on sharing biodiversity information andon the Integrated Publishing Toolkit (IPT2), was alsoorganized by TaiBIF back-to-back with the regional
nodes meeting. The workshop was funded by GBIF
and Taiwan National Science Council, and held at the
Taiwan Endemic Species Research Institute, Jiji Town,
central Taiwan, from 25-27 June. Presentations fromthe workshop are available at http://taibif.org.tw/en/
ipt2012/en-agenda.
The African nodes met for the third time on 17 and
18 July in Kigali, Rwanda. The meeting was hosted
by the Albertine Rift Conservation Society (ARCOS),in collaboration with the Centre for Geographic
Information Systems of the National University

Aug 2011no 29 July 2012

Three GBIF mentoring projects selected
for funding in 2012
Three projects have been selected to receive support
through GBIF’s 2012 mentoring programme, aimed
at sharing expertise and technical support between
participants to stimulate development of biodiversity
information facilities.

The regional meeting of African nodes in Kigali, Rwanda. 
Photo: Fabian Haasof Rwanda. Fifteen African country nodes andinternational organizations participated in themeeting. Highlights included:• Progress with implementing the action plan for
the region, and discussion of the establishment of
an African Coordinating Mechanism, to include adata mobilization strategy, capacity development
and advancing the regional engagement
framework.
• Proposal for an Africa Science Committee,
addressing key research questions and priority
areas for the region, as well the biodiversity
informatics research agenda.
• Recognition of increasing node-to-nodecollaborations within Africa.
The third meeting of the North American nodes
took place in Washington DC at the Smithsonian
Institution’s National Museum of Natural History the
23-24 July, and was co-hosted by the Smithsonian,
U.S. Geological Survey, Integrated Taxonomic
Information System, Consortium for the Barcode ofLife, Encyclopedia of Life, and NatureServe. Twentythree people participated in the meeting with anadditional seven online participants, representing a
total of 22 organizations. Highlights included:• Agreement to develop a regional strategy, basedon the goals expressed in the GBIF 2012-16
Strategic Plan. Major objectives will be to foster
joint collaboration between organizations on
informatics development, content mobilization
and use, and community engagement.
• Node managers and invited speakers identified
plants and invasive alien species as possible
candidates for a regional thematic focus, and plan
to utilize the region’s strengths in genomic andtaxonomic expertise to continue furthering the
GBIF network.

In the first project, GBIF Japan will help theIndonesian Institute of Sciences, which hosts
the national node, to establish a network for the
management of biodiversity information. The
Japanese node will provide training for Indonesiancolleagues to help develop a national plan for
managing and publishing data.
In addition to support provided from core GBIF
funds, GBIF Japan is to receive six million Yen (about€63,000) over three years from Tokyo’s National
Museum of Nature and Science, for mentoring
projects primarily in Southeast Asia, with an initial
focus on Indonesia.
In the second mentoring project, the Atlas of Living
Australia (ALA) will act as mentor to Costa Rica’s
national biodiversity body INBio. The collaboration
will help define a national strategy and action plan tomobilize and publish data through Costa Rica’s GBIF
node. A national workshop on biodiversity informatics
is planned, and a group of software developers from
INBio will be trained to adapt technology developedby ALA to suit Costa Rica’s needs.
In the final project, the South African Biodiversity
Information Facility (SABIF) will act as mentor to ICLEI,
a global network of local governments whose Local
Action on Biodiversity centre is based in Cape Town.
Staff from about 20 local governments from cities
around the world will be trained in using tools andstandards supported by GBIF to enable biodiversity
data to be published and freely accessed. As partof the project, a workshop for data publishers fromlocal governments will be held during the Cities andBiodiversity Summit in Hyderabad, India in October.
Read more…

Translations available for key documents
New translations of the GBIF Memorandum ofUnderstanding are now available in Portuguese andFrench, thanks to voluntary efforts by the Brazilian
Ministry of Science, Technology and Innovation (MCTI)
and GBIF Canada respectively. They supplement an
earlier translation of the MoU into Spanish carriedout by GBIF Mexico. Translations of the GBIF Strategic
Plan (2012-2016) have also been contributed in
French (by GBIF Canada) and Traditional Chinese (byTaiBIF). All the documents are available here …

55GBitsAdditionally, SIB Colombia, which hosts the nationalnode, has translated the manual for the Integrated
Publishing Toolkit into Spanish. The manual isavailable at http://www.gbif.org/orc/?doc_id=4708.

AROUND THE NETWORKSouth African citizen science portal
launched at forum
The South African National Biodiversity Institute(SANBI) has launched a portal enabling the public torecord and exchange information about biodiversity.
The iSpot southern Africa portal is operated incollaboration with the United Kingdom’s Open
University which set up the iSpot citizen science
platform in 2008.
SANBI, which hosts the GBIF node in South
Africa (SABIF), officially launched iSpot southern
Africa during the fourth Biodiversity Information
Management Forum, held at Kirstenbosch near Cape
Town in June. It was followed by a ‘bioblitz’ at the
nearby Kenilworth Racecourse Conservation Area
in which scientists and around 150 members of the
public photographed as many plant, animal andfungus species as possible and posted the data on theiSpot portal.
The forum brought together 29 South African and 16
international organizations. Museums and institutes
receiving grants through SABIF to digitize theircollections showcased their work. SABIF also hosted a
training course on data quality.

Canadensys explorer launched
The Canadensys data repository has launched a new
explorer tool, which allows users to explore, filter,visualize and download all the specimen records
published through the Montreal-based network.

The Canadensys explorer currently aggregates 15
published collections, comprising over 600,000
occurrence records of which nearly 80% are from
Canada. All of the records are served to the GBIF
network using the Canadensys Integrated Publishing
Toolkit (IPT).
6

6

Public invited to contribute to atlas of
Irish mammals
The National Biodiversity Data Centre (NBDC)
in Ireland is asking the public to help record the
distribution of wild mammals in the country and its
surrounding seas. The Atlas of Mammals in Ireland
project compiles data from existing recording
initiatives, presenting species accounts anddistribution maps. A primary aim is to encourage
recording of the more common Irish mammals to help
draw up a comprehensive picture of their distribution
by 2015, acting as a baseline against which to monitor
future change.
An account of the ‘great Irish mammal watch’appeared in the Irish Times on 5 July.

GBIF showcased at public science eventin Germany
Interested public had the opportunity to get an insight
into biodiversity informatics and GBIF Germany
at the Berlin Night of Science “Lange Nacht derWissenschaften”. A 20-minute talk on science data
in GBIF, short films on GBIF-related projects andguidance on using the GBIF portal were given at the
Natural History Museum (Museum für Naturkunde,
MfN) and the Botanic Garden and Botanical Museum
Berlin-Dahlem (BGBM).

INFORMATICS
Task group to develop standard forspecies descriptions
A new task group for Biodiversity Information
Standards (TDWG) is being set up to take forward thePlinian Core set of descriptors, enabling information
about species to be shared and integrated.
The Plinian Core provides standardized descriptors
for species reproduction, behaviour, lifecycle, feeding
and other information. It was adopted by the InterAmerican Biodiversity Information Network (IABIN),
and used to import species information into theEncyclopedia of Life (EOL). The standard is now to be
developed further as a community effort, throughthe task group open to all interested. The group is
expected to be formed in time for the 2012 TDWG
annual meeting from 22-26 October in Beijing.
The task of bringing the Plinian Core to the next level
was discussed at a meeting hosted by CONABIO, theGBIF node in Mexico.

New tool for analysing datasets
published through GBIFThe University of Navarra in Spain has developed
an online tool to visualize the content of datasets
published to the GBIF network. The BIoDiversity

Aug 2011

DataSets Assessment Tool (BIDDSAT) helps potential
users to assess the fitness for use of datasets andbring up issues for correction.
The online application is accessible at http://www.
unav.es/unzyec/mzna/biddsat/ and is supported by
all major browsers. A description of the tool was
published in the Bioinformatics journal in June.

Darwin Core Archives now just a click
away with BioCASe 3.2

no 29 July 2012

The objective of the pilot projects is to place as
many new scientific names from Global Partners as
possible in taxonomic checklists and, then, supply
them to the Catalogue of Life during routine updates.
Unincorporated names will be returned to i4Life withannotations to show their status.
The i4Life budget commits approximately €200k plus
overheads for this purpose and the duration of thepilot projects will be 5 months. Eligibility criteria aregoverned by European Commission rules.

The development team at the Biological Collection
Access Service (BioCASe) has released a new versionof its BioCASe Provider Software. Information
published using the new version, BioCASe 3.2, can beeasily stored as XML or Darwin Core Archives.

More information is on the i4Life webpage: http://i4life.eu/pilots.php

With the new archives supported by BioCASe,
harvesting and indexing processes will be more
efficient and less error-prone. Data publishers can
now easily switch between using the simpler Darwin
Core standard and the richer Access to BiologicalCollections Databases (ABCD) schema. For more
information on BioCASe and the new software
version, visit http://www.biocase.org.

3rd European Congress of Conservation
Biology (ECCB 2012)

OPPORTUNITIES

6-15 September 2012, Jeju, Republic of Korea
More information…

i4Life call for Pilot Projects – building
content for the Catalogue of Life

14th Annual BIOECON Conference

Deadline: 31 August 2012 - 12:00 am (midnight, Paris
local time).
The i4Life project is offering funding to establish andimplement i4Life Pilot Projects to enhance taxonomic
content of Global Species Databases (GSD) thatwill check and incorporate in their databases newscientific names and taxa, harvested from Global
Partners (GBIF, IUCN Red List, BOLD, EMBL ENA and
Encyclopedia of Life).

UPCOMING EVENTS
28 August - 1 September 2012, Glasgow, United
KingdomMore information…

IUCN World Congress 201218-20 September 2012, Cambridge, United Kingdom
More information…

19th meeting of the GBIF Governing
Board (GB19)
16-21 September 2012, Lillehammer, Norway
More information…

Biodiversity Technologies Symposium
27-28 September 2012, Oxford, United Kingdom
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/

GBits archive: http://www.gbif.org/communications/
resources/newsletters/
77