GBits

no. 26 Jan 2012

GBIF COMMUNITY � � � � � � � � � � 2free and open access to biodiversity data

First GBIF Data Paper
published
The first-ever peer-reviewed paper derived directly from abiodiversity metadata document has been published in theopen-access ZooKeys journal.
The description of more than 2,400 bird records from
northeast India, spanning almost a century, is the outcomeof a new ‘Data Paper’ workflow pioneered by GBIF andPensoft publishers.
The aim is to provide incentives for those compiling datarecords about the occurrence of species to make their
existence known to the scientific community, thus helping
to increase knowledge about biodiversity and inform
conservation measures.
Photo: J.M. Garg (Wikimedia Commons)Second version of Ireland’s Biodiversity Maps
released
Project takes shape to digitize camera trap data

DATA PUBLISHING NEWS � � � 2
New biodiversity data publishing framework
proposedGerman research team targets ‘at risk’ data onbiodiversity
New publishers

INFORMATICS � � � � � � � � � � � � � � 4
New BioCASe version speeds large dataset
harvesting

GBIF SECRETARIAT NEWS � � 4
TRAINING AND
COLLABORATION � � � � � � � � � � � 4Call for applications for regional training support
GBIF Spain’s training programmes in 2012
Call for 2012 GBIF Mentoring Programme

AWARD NOMINATIONS� � � � � � 5Call for nominations for the 2012 Ebbe Nielsen
PrizeCall for proposals for the 2012 Young ResearchersAward

UPCOMING EVENTS � � � � � � � � 5
13th annual meeting of the Society of BiologicalSystematics, GermanyWorkshop on genomic data standards
Oriental White Eye (Zosterops palpebrosus), one of the species documented in the new Data Paper.

A Data Paper is produced when metadata (data aboutdata) are compiled using the GBIF Integrated Publishing
Toolkit (IPT) generating a manuscript that then goes
through the usual critical review process before being
accepted for publication.
Read more…

GBits
GBIF COMMUNITY

Project takes shape to digitize camera
trap data

Second version of Ireland’s Biodiversity
Maps released

An Indo-Norwegian project to make available camera
trap data from India could help conservation of tigers,
leopards, elephants and snow leopards.

Ireland’s GBIF Node, the National Biodiversity Data
Centre, has released the second version of its online
data portal Biodiversity Maps.
The system, built on an ESRI geographic information
system (GIS) platform and using Microsoft Silverlight
software, now provides the biodiversity mappingneeds for the terrestrial and marine environment ofIreland.
Eighty datasets, comprising two million observationsof 12,000 species (one third of all known Irish species)
are now mobilized, and feeding automatically into theGBIF data portal.

The species are being targeted in a partnership
between India and Norway to demonstrate capacity
building under the new Intergovernmental SciencePolicy Platform on Biodiversity and Ecosystemservices (IPBES).
Priorities for the project, which GBIF is helping
to facilitate, emerged at a meeting in New Delhi
involving senior government representatives from thetwo countries.
The two-year pilot project will demonstrate how
decision-makers can use data gathered from cameras
equipped with motion sensors to photograph passing
animals. It will focus on developing strategies for theconservation of tigers and elephants in the Rajaji
National Park, leopards in Maharashtra and snow
leopards in Sikkim. It will also help show the benefitsof data sharing in India by developing user-friendly
maps and GIS-data products adapted to various
users including decision makers, researchers and civilsociety groups.
Read more…

DATA PUBLISHING NEWS
Screenshot of Ireland’s new biodiversity map interface.

Three key features have been developed:• A terrestrial and marine mapping system,
integrating different geographic projections, sothat all biodiversity data for the island of Irelandand its marine waters out to 1,000 kilometres canbe mapped together.
• A system enabling registered users to report on
the biodiversity interest of a given area, helping
to inform decision-making. These user-defined
reports can be generated for scales ranging from
50 square kilometres down to less than a hectare.
• Habitat maps, integrated to complement species
observations. The National Parks and Wildlife
Service, Ireland’s statutory nature conservation
body, has completed an extensive programme ofnational surveys of Ireland’s protected habitats,and the first of these have been mobilized
through the data portal.
For further details contact Liam Lysaght, Director,
NBDC (llysaght@biodiversityireland.ie)
22New biodiversity data publishingframework proposed
A comprehensive framework to encourage andfacilitate the sharing of biodiversity data has been
published in a peer-reviewed journal.
The 24 recommendations of the GBIF Data
Publishing Framework Task Group are included in a
special supplement of BMC Bioinformatics. These
recommendations target social, cultural, technical,
policy, legal, economic components to promote data
sharing.
Separate papers in the BMC Biodiversity Informatics
supplement cover: the ‘data paper’ mechanism;
indicators for a Data Usage Index; an index forbiodiversity informatics potential of countries; andproposals for a data hosting infrastructure.
Read more…

Aug 2011

German research team targets ‘at risk’data on biodiversity

A new German-based project is setting out to rescue
biodiversity data at risk of being lost, because they
are not integrated in institutional databases, arekept in outdated digital storage systems, or are notproperly documented.
The project, run by the Botanic Garden and BotanicalMuseum Berlin-Dahlem, provides a good example fora GBIF recommendation to establish hosting centres
for biodiversity data. This is one of a set of datamanagement recommendations just published byGBIF.

no 26 Jan 2012teacher of the father of modern taxonomy, CarlLinnaeus.
http://data.gbif.org/datasets/resource/13718
Belgium - Another major historic collection, from theRoyal Belgian Institute of Natural Sciences, has madeits debut on the GBIF portal. More than 320,000
records covering 73,000 animal taxa with a wide
geographic and taxonomic range are included in theDaRWIN (Data Research Warehouse Information
Network) database. Constantly expanding, DaRWIN
is just a glimpse of a vast collection with its origins in
the 18th century, currently estimated to include some37 million specimens of zoological, anthropological,paleontological, mineralogical and geologicalmaterials.
http://data.gbif.org/datasets/resource/13690
France - The Muséum d’Histoire Naturelle de Bourges,
has published 430 mammal records of 163 taxa.
http://data.gbif.org/datasets/resource/13710
Switzerland - The Musée Cantonal de Zoologie in
Lausanne has published 103 records from its insect
and mollusc collections dating back to the mid-19thcentury. http://data.gbif.org/datasets/resource/13712

Valuable biodiversity data are held on outdated 3.5” floppy disks.

The team behind the German project called reBiND,or Biodiversity Needs Data, has started identifying
threatened databases for archiving, and will makethem accessible via the GBIF network.
Read more…

New publishers
Estonia - The Natural History Museum of theUniversity of Tartu has published a large numberof records from its databases on animal, plant andfungal specimens from Estonian collections. It is thefirst time non-fossil biodiversity data hosted in Estonia
have been published since the country became a GBIF
Participant. Until now, only paleontological collections
have been available through the Data Portal. Some
90,000 records can now be accessed. They include
more than 4,000 kinds of fungus, 1,200 plant and1,100 animal taxa. The records come from specimen
collections of the museum itself, Estonian Universityof Life Sciences and the Tallinn Botanical Garden.
http://data.gbif.org/datasets/resource/13670
http://data.gbif.org/datasets/resource/13671
http://data.gbif.org/datasets/resource/13672
Sweden - Records from one of the world’s oldest andmost important insect collections, based at Lund
University, are now accessible through the GBIF Data
Portal. The Lund Museum of Zoology has published adataset of around 140,000 specimens including over
72,000 insect taxa. The collection dates back to 1735,
with its first donation coming from Kilian Stobaeus,

Australia - The Western Australian Herbarium has
published nearly three quarters of a million plant
records, in a dataset presenting an inventory of theflora of Western Australia. It contains taxonomic,
geographical and ecological information based on theherbarium’s specimen collections.
http://data.gbif.org/datasets/resource/13675
Canada - The Université de Montréal BiodiversityCentre has published more than 135,000 recordsof plant specimens held in the Marie-VictorinHerbarium. The dataset covers the digitized portionof the fourth largest Canadian herbarium, which
includes more than 620,000 vascular plants and50,000 bryophytes (mosses and worts), around half
originating from Canada.
http://data.gbif.org/datasets/resource/13734
A Canadian-based citizen science service, Wildlife
Sightings has begun publishing data to the GBIF
network. It was inspired by the Thousand Eyes
Project, recalling the pioneering work of a school
superintendent in Nova Scotia who encouraged
schoolchildren to compile nature observations,recorded by nib pens and entered in ledgers. Wildlife
Sightings updates the process using GPS devices
and digital photos to help validate the observations.
http://data.gbif.org/datasets/resource/13709
United States - The New York State Museum inAlbany, NY, has published more than 14,000 recordsof the museum’s mammal specimens. These include
skins, skeletons, fluid preservations and frozen tissue
from 250 mammal species, mostly from the state ofNew York.
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http://data.gbif.org/datasets/resource/136663

GBitsThe Cincinnati Museum Center has published nearly
10,000 records of reptiles, amphibians and birds fromits herpetological and ornithological collections. The
herpetological data are from vouchered specimens
held in the museum, while the bird records include
frozen tissues, blood samples and isolated DNA.
http://data.gbif.org/datasets/resource/13711
http://data.gbif.org/datasets/resource/13990

on investment for the verysmall core budget it operates
on. The main challenge going
forward is for the Participants,
the founders and owners ofGBIF, to take greater ownership,
direct GBIF to meet theirneeds and derive the greatest
benefit and optimal return fromtheir establishment of, andparticipation in GBIF.

The Fish division of Ohio State University’s Museumof Biological Diversity has published nearly 90,000
records of almost 900 fish taxa, concentrated on
species found in Ohio’s lakes, rivers and streams but
extending across the eastern United States.
http://data.gbif.org/datasets/resource/13717“I wish you and GBIF all success in the future andthank you for all the inputs and contributions over thepast few years.”

INFORMATICSTRAINING AND COLLABORATIONNew BioCASe version speeds largedataset harvesting

Call for applications for regional training
supportA new version of the BioCASe Provider Software
will enable very large datasets to be harvested
more quickly by networks such as GBIF. Version 3of the software, released in December, allows all
information published by a BioCASe provider to be
stored in a single XML file. If required, these files canbe transformed in a subsequent step into Darwin Core
Archive, the preferred format for serving data to GBIF.

The GBIF Secretariat calls for applications from
Participants seeking support to organize regional
training activities in 2012.

This feature will be especially useful for datasets
containing millions of records, as it will enable more
efficient harvesting and reduce the time needed forGBIF and other networks to index new or updated
data from publishers using BioCASe.
The Biological Collection Access Service (BioCASe) is
a suite of standards and software tools for sharing
rich information from natural history collections andobservation databases. They are grouped around thecomprehensive Access to Biological Collections Data(ABCD) schema and the BioCASe Provider Software
for publishing biodiversity knowledge.
More information on BioCASe and the new BioCASe
Provider Software is available at http://www.biocase.
org and http://wiki.bgbm.org/bps.

GBIF SECRETARIAT NEWSAt the end of December, GBIF bade farewell to Nick
King its Executive Secretary. As reported in the lastGBits, he is replaced by Donald Hobern, until now
director of the Atlas of Living Australia.
In his farewell message to GBIF participant countries
and organizations, Nick says, “The past four and ahalf years as Executive Secretary have been very
exciting, as well as somewhat frustrating. GBIF isnow in great shape, and delivering an excellent return
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GBIF Participants are invited to apply for financial
support of up to 5000 EUR per event, to be used
exclusively to enable regional participation in theirevents, by representatives of GBIF Participants fromthe region. These may be either trainers or trainees.
For further details, please download the full call forapplications.

GBIF Spain’s training programmes in 2012
GBIF Spain is organizing 11 training events in2012, which may be of interest to the wider GBIF
community. Training programmes include those on
persistent identifiers, data quality in biodiversity
databases, GIS, sensitive data management, data
recording for technicians working with natural
history collections and sharing digital images fromcollections.
A full list of events is at http://www.gbif.es/Plan_formacion_in.php.

Call for 2012 GBIF Mentoring Programme
GBIF invites nodes to submit proposals for the 2012
Mentoring Programme. The deadline for submission is30 March 2012, and nodes are encouraged to contact
each other directly to explore possibilities of joint
mentoring activities.
All information about the mentoring programme andthe application guidelines are available at http://www.gbif.org/participation/participant-nodes/
mentoring/call-for-mentoring-proposals/Aug 2011no 26 Jan 2012

AWARD NOMINATIONSUPCOMING EVENTS

Call for nominations for the 2012 Ebbe
Nielsen Prize

13th annual meeting of the Society ofBiological Systematics, Germany

GBIF invites nominations for the 2012 Ebbe Nielsen
Prize, awarded annually to a person or team who
demonstrates excellence in combining biodiversity
informatics and biosystematics research.

Bonn, Germany, 23-25 February 2012The €30,000 award is intended to allow therecipient(s) to engage in biosystematics/biodiversityinformatics research outside his/her/their country ofresidence for a period of three to six months.
Nominations are due by 15 March 2012. Individuals
or institutions who wish to be nominated should
contact the Head of Delegation of the relevant GBIF
Participant country.
For further details, please download the full call for
nominations (pdf file, 38 KB)

Call for proposals for the 2012 Young
Researchers Award
GBIF invites proposals from graduate students
for the 2012 Young Researchers Award. This prize
intends to foster innovative research and discovery inbiodiversity informatics.
Two awards of €4,000 will be available to graduate
students in a master’s or doctoral programme at auniversity in a GBIF Voting Participant or Associate
Participant country.
Submitted proposals will be reviewed by the Head ofDelegation of a GBIF Voting or Associate Participant
country.
The deadline to receive nominations from the Heads
of Delegation is 15 March 2012.
For further details, please download the full call for
proposals (pdf file, 84 KB).

Three GBIF-related projects will be presented at
the meeting of the Gesellschaft für BiologischeSystematik (GfBS). The three projects are the Diversity
Workbench, which is a database system to store
different types of bio- and geodiversity data; the DNA
Bank Network, a non-commercial scientific service
based on the GBIF infrastructure and the BiologicalCollection Access Service to provide access to
information associated with organisms’ DNA samples;
and the Senckenbergische SAMmlungsmanagementSystem (SeSAM), a collection management system
which documents the relationship between objects
and theories.

Workshop on genomic data standards
Oxford e-Research Centre, UK, 27-29 February 2012
GBIF is organizing a workshop, in collaboration with
the Genomic Standards Consortium (GSC), on specieslevel biodiversity and genomic data standards withthe aim of ensuring alignment and harmonization ofefforts. The workshop will contribute to the ongoingwork of the USA National Science Foundation-funded
Research Coordination Network, which seeks topromote the integration of genomic standards withecological and species level standards.
The GSC is an international community that promotes
mechanisms for standardizing descriptions ofgenomes and especially the contextual information(e.g. environmental variables) associated withgenomic samples.
For further information, contact Dr Éamonn Ó Tuama,
GBIF Secretariat (eotuama@gbif.org).

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 ØDenmark

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/
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