GBits

no. 24 Sep 2011

SCIENCE AND POLICY � � � � � � 2free and open access to biodiversity data

Preserving biodiversity
knowledge from impact
assessments
Professionals assessing the environmental impact ofproposed large projects are being urged to share thebiodiversity data they generate.
A new Best Practice Guide produced by GBIF and theInternational Association for Impact Assessment (IAIA)
explains the straightforward steps required to ensure thatbiodiversity data remain accessible for future decisionmaking, scientific research and society as a whole.

GBIF data network helps map medicinal plants inAustralia
Launch of new open access journal on invasive
alien species
New Biodiversity Hub aims to integrate open
access research, primary data and other species
information

INFORMATICS � � � � � � � � � � � � � � 2
New GBIF Data Portal developments available fortesting

GBIF COMMUNITY � � � � � � � 3, 4Book on Tanzania species checklist to be launchedsoon
DanBIF website hosts information on over 31,000
Danish species
First meeting of GBIF Germany’s IT commission
New Zealand Virtual Herbarium launched
EOL version 2 launched, incorporating updated
GBIF species occurrence maps
Regional meeting of GBIF African nodes
Symposium on biodiversity informatics held in
Bogotá
New initiative to provide free access to Albertine
Rift biodiversity data via web portal

DATA PUBLISHING NEWS � � � 5
New publishers from Belgium, Benin and Guinea
Other datasets of squirrels from Scotland andfrom Japan’s prefectural museums
Highway bridge and tunnels under construction in Andorra

RELATED NEWS� � � � � � � � � � � � � 5

The guide was prepared in response to concern that vital
data on occurrence of species at and around a proposed
project site, gathered in the preparation of environmental
impact assessments (EIAs), are often discarded and lost at
the end of the project planning process.

White House science advisers call for new ecoinformatics body and strengthened links with GBIF

Pilot projects in South Africa and India have helped todevelop tools to facilitate the publication of biodiversity
data from EIA through the GBIF network, making them
freely available via the Internet.

Strategy for English biodiversity to 2020 launched

US$ 10 million grant from NSF to coordinate
digitization of biodiversity collections in 45 US
statesUPCOMING EVENTS � � � � � � � � 6
Training course on biodiversity data publishing andfitness for use in the GBIF Network

Publishing EIA-Related Primary Biodiversity Data: GBIFIAIA Best Practice Guide (pdf file, 1.8 MB) and a summary
version are now available for download.

GBIF Science Symposium 2011

It provides a step-by-step guide for environmental
assessment professionals, explaining the process of
selecting software tools, preparing datasets and publishingthem according to agreed global standards and protocols.

Biodiversity data analysis and use workshop by
GBIF France

Read more...

Biodiversity data and information management
principles course by ARCOS

Training course on persistent identifiersGBitsSCIENCE AND POLICY
GBIF data network helps map medicinal
plants in Australia
Innovative use of data accessible through GBIF may
help to identify areas of high cultural value, basedon plants used in traditional medicine by Aboriginal
people in Australia.
The Customary Medicinal Knowledgebase (CMKb),
based at Macquarie University, is teaming up with theAtlas of Living Australia (ALA), which hosts the GBIF
national node, to integrate medicinal knowledge withother information on Australian biodiversity.
A recent study modelled suitable ecological niches
for more than 400 plant species that are of medicinal
importance, using data accessed through the GBIF
portal and Australia’s Virtual Herbarium (AVH), one of
the main resources contributing data to ALA.
The outcome of the study, published in the journal
Ecological Modelling, was a map of potential “biocultural diversity hotspots”, areas suitable for theoccurrence of multiple species known to be used in
traditional medicine.

Banksia integrifolia

The lead author, Jitendra Gaikwad of Macquarie
University, said: “This methodology allows us toevaluate the cultural value of the land. We haveused medicinal value, but we can use other socioeconomic, traditional knowledge and biodiversity
conservation aspects as well.”Read more…

Launch of new open access journal oninvasive alien species
A new open-access journal specializing in invasive
alien species, from GBIF partner Pensoft Publishers,
was launched in early September. The journal
NeoBiota continues the former NeoBiota Proceedings
series, and provides automated cross-linking throughthe Pensoft Taxon Profile tool revealing all taxa
published.
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New Biodiversity Hub aims to integrate
open access research, primary data andother species information
The Public Library of Science (PLoS), the nonprofit
open-access scientific publishing project, haslaunched a Biodiversity Hub aiming to accelerate
the discovery, dissemination and integration of
biodiversity studies.
The Biodiversity Hub provides three general services.
First, it builds on the idea of open access publication
by aggregating selected open access journal articles
focused on biodiversity science. Second, the Hubadds value to previously published content. Third, it
provides a community forum for interaction around
specific content. Commentary and links to researchresources and community projects can attract users
and broaden support for biodiversity initiatives.

INFORMATICSNew GBIF Data Portal developments
available for testing
GBits subscribers are invited to test recent
improvements to the GBIF Data Portal. They are
aimed at providing richer taxonomic content,
reducing errors and speeding up processing.
Key improvements include:• reduced processing time from 3-4 days to around36 hours, allowing for more frequent index
updates, so reducing time lag between data being
added or changed, and becoming visible on the
portal;• a complete reworking of the backbone taxonomy
with up-to-date checklists and taxonomic
catalogues enabling better-organized content;• indexing of checklists published throughthe Global Names Architecture profile, aninternational standard for sharing taxonomic data
based on the GBIF-endorsed Darwin Core Archive
format;• authorship and common names for higher taxa
included where available; and• enhanced data interpretation routines andplausibility checks, helping to flag data withapparently incorrect locations, dates, altitude, etc.
Please check out the results at http://testportal.gbif.
org and send us your feedback. When viewing thetest site, please make comparisons with the existing
Data Portal, and consider whether the principal goal,
improving the content available, has been achieved.
In this phase of development, our focus has beenon improving existing processing routines. Future
developments, to be rolled out next year, will see
the index enriched with more content types, and theportal’s functionality will be expanded.

Aug 2011

GBIF COMMUNITY
Book on Tanzania species checklist to belaunched soon
Tanzania Biodiversity Information Facility (TanBIF)
is launching a book on its checklist of over 24,000
Tanzanian species, a major outcome of a GBIF
capacity enhancement programme.
The book, which will also be available electronically,
will be published on 10 November. The checklist it
describes is the result of a €400,000 project under
the GBIF Capacity Enhancement Programme forDeveloping Countries (CEPDEC), led by the Tanzania
Commission for Science and Technology (COSTECH)
and funded by the Danish Ministry of Foreign Affairs.
The project aimed to enhance access to andutilization of data on Tanzania’s biodiversity, held innatural history museum databases within and outside
the country.
Another of the main outcomes of the project was
the development of the TanBIF portal which sharesbiodiversity information for policy, management,
research and education.
The CEPDEC project also helped develop the QGISTanBIF decision-making tool, based on open source
software. This tool enables analysis of primarybiodiversity data to support biodiversity-related
decision-making in activities such as land-use
planning, design of protected areas, conservation andsustainable use strategies, risk assessments, climatechange impact assessments, etc. Ninety-five people,
including trainers, have been trained in the use of thetool in a series of workshops, and TanBIF has issued
a call for showcases on the application of the tool in
biodiversity decision-making.
A video that explains the uses of the tool anddemonstrates its installation is available at http://
www.gbif.org/orc/?doc_id=2970.

DanBIF website hosts information onover 31,000 Danish species
The Danish Biodiversity Information Facility has
developed and houses a number of websites. One ofthem, www.allearter.dk, now lists more than 31,000of the estimated 35-40,000 species occurring in
Denmark. According to Isabel Calabuig, the Danish
node manager, “The number of species listed
increased by about 10,000 in the last month, andthe lists are improved and are now downloadable”.
The site is expected to include information on some
35,000 species. With the help of experts, the site
provides a platform to help avoid inconsistencies in
the use of Danish and scientific names of species inscientific literature, municipal records and collections.

no 24 Sep 2011

DanBIF has also launched a multimedia server –www.multimedia.danbif.dk – a space for presenting
photographs, videos, sound files and literature on
biodiversity. The system makes it possible to publish
files with curatorial information and georeferences.
As the GBIF Data Portal can only link its records
to images, these files need to be stored on awebserver. DanBIF’s multimedia server provides
access to multimedia information according to GBIF
guidelines. In September, two of the most important
Danish botany journals were made available online
through the multimedia server, to be included in the
Biodiversity Heritage Library.

First meeting of GBIF Germany’s IT
commission
GBIF Germany’s IT Commission held its first meetingon 23 September at the Botanic Garden and BotanicalMuseum (BGBM) in Berlin. A new image data server,
installed at the BGBM, was presented at the meeting.
One of the functions of the IT Commission isto define the services provided by the Germannode institutions, and to coordinate common
developments.
Eight nodes form GBIF Germany, each responsible
for a range of taxonomic groups. Participantsfrom each of the node institutions attended themeeting to discuss the use and processing of image
data within the GBIF Germany research project
Kompetenzzentren innovativer Datenmobilisierung(Competence centres for innovative data
mobilization).
The main objective of the project is the mobilizationof data from Germany’s research community, focusing
on species occurrence data. The funding has allowed
investment in technical infrastructure such as a stabledata hosting system and the image data server.

New Zealand Virtual Herbarium launched
The New Zealand Virtual Herbarium has beenlaunched, providing free Internet access to about half
the records held by 11 botanical collections across thecountry.
The eleven herbaria house nearly 1.5 million
specimens of mosses, lichens, liverworts, ferns, algae
and seed plants that have been collected in New
Zealand from 1769 (Captain Cook´s first voyage) tothe present day.
Some of the participating members of the Virtual
Herbarium project, the Allan Herbarium and the
National Fungal Herbarium, both operated by
Landcare Research, publish their data through the
GBIF data portal.
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GBits
EOL version 2 launched, incorporating
updated GBIF species occurrence maps
The second edition of the free, online collaborative
Encyclopedia of Life (EOL) is now available, with aredesign and new features making it easier to use,
personalize, and to interact with fellow biodiversity
enthusiasts worldwide.
EOL, an associate Participant of GBIF, includes mapsof occurrence records published via the GBIF networkon each of its 750,000 species pages. Thanks to
the ongoing collaboration between GBIF and EOL,
the new version is able to display data recently
updated from the GBIF Data Portal, and software
improvements will enable the information visible on
the EOL data maps to be regularly refreshed.
With the new EOL interface, users can more easilyfind species of interest; create personal virtual
collections of photos and information; find or upload
pictures, videos and sounds; and share comments,
questions and expertise with users who share similarinterests.

Regional meeting of GBIF African nodes
Delegates from African GBIF nodes met on 13 and 14
September to identify priorities and actions required
for advances in science and biodiversity informatics
on the continent. This was the second regional
meeting for Africa, part of the growing process ofregional collaboration between GBIF Participants.

Studies: Present and Future, on 8 August 2011. The
main themes of the symposium were developmentsin the field of biodiversity informatics in Colombia andabroad, and the use of bibliometrics to analyse trends
in biodiversity studies.
The symposium was part of a year-long programmeof activities to commemorate the 75th anniversary of
the Instituto de Ciencias Naturales.

New initiative to provide free access toAlbertine Rift biodiversity data via web
portalData and information from one of Africa’s mostsignificant and threatened areas for biodiversity willsoon be fully available and freely accessible via theInternet.
The Albertine Rift Biodiversity Portal initiative, led by
the Albertine Rift Conservation Society (ARCOS), aims
to improve decision-making in this globally importantregion for biodiversity, which includes the Virunga
National Park, home to mountain gorillas.
ARCOS has secured funding from the JRS Biodiversity
Foundation, to establish a regional databasedriven website and an informative, educational
web portal. GBIF, which includes ARCOS as an
Associate Participant, is providing expertise on thetools required to make species occurrence records
accessible via the portal.

Twenty-eight delegates representing 18 country
and organizational nodes attended the meeting at
the National Botanical Gardens in Pretoria, South
Africa. It was hosted by the South African Biodiversity
Information Facility (SABIF) and funded by the
Department of Science & Technology.
Three priority areas of work identified for regional
collaboration and partnership over the next two years
were capacity building, data publishing and regional
node activities. Key outputs were identified and will
be finalized by the relevant task teams and leaders
established for each work area.
Selwyn Willoughby, Director of Biodiversity
Information Management at SANBI, said: “We areworking towards the practical implementation ofactions that would ensure that the data we manage
contributes towards initiatives beyond the GBIF
community, such as the 2020 Aichi Biodiversity
Targets.”

Symposium on biodiversity informatics
held in Bogotá
The Instituto de Ciencias Naturales of the Universidad
Nacional de Colombia in Bogotá hosted a symposium
entitled The Impact of Informatics on Biodiversity
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Mountain Gorilla, a species found in the Albertine Rift region

The Albertine Rift Biodiversity Portal will be
developed in collaboration with a consortiumof leading institutions in the field of data andinformation management in the region (national
data centres in Uganda, Rwanda, DRC, Burundi andTanzania; TanBIF and GBIF Uganda) and outside theregion (National Museums of Kenya – NMK, GBIF
Secretariat, UNEP-WCMC and UNEP-GRID Arendal).
The project started in July 2011 and runs until June
2013.

Aug 2011

DATA PUBLISHING NEWSNew publishers
Florabank, a database with more than three million
records of Belgian plants, is now accessible via the
GBIF data portal. Belgium’s Research Institute for
Nature and Forest (INBO), a scientific institute of
the Flemish Government, published the database of
distribution data on the wild flora of Flanders and theBrussels region. The records relate to the distributionof vascular plants from 1800 until today.
Florabank also contains an ecological database withdata such as IUCN Red List category information,legal protection, global distribution, seed bank, etc.
The database is an initiative of the Flo.Wer NGO,
the Research Institute for Nature and Forest andthe National Botanic Garden. (http://data.gbif.org/
datasets/resource/13458)
Benin’s Université d’Abomey-Calavi has published7,397 records of plants from the National Herbariumof Benin, based at the university. (http://data.gbif.
org/datasets/resource/13459)
The Centre d’Observation de Surveillance etd’Information Environnementales (COSIE), Guinea’s
National Centre for Environmental Information
Monitoring published 493 records of flowering plantsfrom a 2008 inventory from the Mount Nimba area.
(http://data.gbif.org/datasets/resource/13405)

Other datasets
The UK’s National Biodiversity Network has
published 36,031 records from the Scottish Wildlife
Trust’s Scottish Squirrel Database (http://data.gbif.
org/datasets/resource/13407). This database is froman ongoing survey to monitor distributions of invasive
grey and native red squirrels throughout Scotland,
helping to identify areas where habitat management
will benefit native populations.
Japan’s National Museum of Nature and Sciencelocated in Tokyo has published 253,730 records fromvarious prefectural, municipal and city museums.

RELATED NEWSWhite House science advisers call for new
eco-informatics body and strengthened
links with GBIFThe United States President’s Council of Advisors
on Science and Technology (PCAST) has proposed a
new national informatics facilitating body, with thesuggested name of ecoINFORMA, closely co-operatingwith a strengthened GBIF and other global data
initiatives.

no 24 Sep 2011

In a report published in July, the advisers note:“The United States should continue to support
and provide data and expertise to the Group on
Earth Observations (GEO) and its Biodiversity
Observation Network (GEO BON), the Global
Ocean Observing System (GOOS), and the Global
Biodiversity Information Facility (GBIF), among otherinitiatives”, to strengthen international global-change
research focused on ecosystem services and theirsustainability.
The report also noted: “Global observing andinformatics systems such as the Biodiversity
Observation Network of the Group on Earth
Observations (GEO BON) and the Global Biodiversity
Information Facility (GBIF), as well as a revitalized
global change research program, are required tosupply the newly-established Intergovernmental
Science-Policy Platform on Biodiversity and Ecosystem
Services (IPBES).”

US$ 10 million grant from NSF tocoordinate digitization of biodiversity
collections in 45 US states
The National Science Foundation (NSF) has awarded
a five-year, US$ 10 million grant to Florida State
University and the University of Florida to coordinate
92 institutions in 45 states working to digitize thenation’s biological collections.
Called Integrated Digitized Biocollections or iDigBio,
the information in the digitized collections will include
field notes, photographs, 3-D images and information
on associated organisms, geographic distribution,
environmental habitat and specimen DNA samples.
The natural history data will be available to anyone
online.

Strategy for English biodiversity to 2020
launched
A plan to create better habitats and join up the
habitats of some of England’s most iconic wildlife has
been published. ‘Biodiversity 2020: A strategy for
England’s wildlife and ecosystem services’ aims to halt
the loss of England’s habitats and species, and follows
up the groundbreaking global agreement reachedat the Convention on Biological Diversity (CBD)
conference held in Nagoya, Japan, in October 2010.
The England Biodiversity Strategy and associateddocuments are available at http://www.defra.gov.uk/
environment/natural/biodiversity/

55GBitsUPCOMING EVENTS
Training course on biodiversity data
publishing and fitness for use in the GBIF
network
Buenos Aires, Argentina, 28-30 September 2011
This training provides GBIF node managers with
up-to-date information about new biodiversity
data publishing options, building data discovery
and publishing strategies and action plans, anddata quality and fitness for use. This event will beheld back-to-back with the global Nodes meeting
associated with the 18th meeting of the GBIF
Governing Board.

GBIF Science Symposium 2011
Buenos Aires, Argentina, 5 October 2011
The annual GBIF Science Symposium, including theEbbe Nielsen Prize Winner Lecture, is being organizedas part of the 18th GBIF Governing Board meeting

and associated events. The symposium is open to the
public, and prior registration is required.

Biodiversity data and information
management principles course by ARCOS
Kigali, Rwanda, November-December 2011
This workshop is being organized in the context
of the project of the Albertine Rift Conservation
Society (ARCOS), to build competence for biodiversity
information systems in the region (read more on theinitiative in the GBIF Community section on page4). The workshop covers data integration, planning,
design and testing.
More information...

Biodiversity data analysis and use
workshop by GBIF France
Paris, France, November 2011
This workshop gives researchers, publishers, andothers in charge of organizing biodiversity information
networks an overview of the different ways to access
GBIF-mediated data as well as various possible uses ofsuch data.
More information...

Training course on persistent identifiers
February 2012
The workshop aims at increasing the knowledgeof teams leading the development of biodiversity
informatics tools on persistent Identifiers. The training
looks specifically at issuing, using, publishing andresolving identifiers.
More information...

Click on image to download brochure (PDF, 891KB)

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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