GBits

no. 30 Sep 2012

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

GBIF Finland
demonstrates ‘assemblyline’ for digitization
A new high-performance system for digitizing natural
history records in Finland aims to convert a thousand plantor insect specimens a day into digital data.
The system is custom-built from conveyor belts andcameras, acquired from various sources (see this video
showing the system in operation).
The ‘assembly line’ has been developed in Joensuu,Finland, by Digitarium, the digitization centre of the FinnishMuseum of Natural History and University of Eastern
Finland, which operates the GBIF national node.

New guide for developing marine species
checklists

TAXONOMY� � � � � � � � � � � � � � � � � 2
Naming of animal species moves into the digitalage

SCIENCE AND POLICY � � � � � � 2
Fourth GBits Science Supplement published

AROUND THE NETWORK� � � � 2
Digital catalogue of New Zealand’s biodiversity
launched
Atlas of Living Australia develops tests to detectsuspect records and duplicates
Ireland’s biodiversity data centre appeals for insectrecords‘New deal’ needed for world’s plants – outgoing
Kew director

TRAINING � � � � � � � � � � � � � � � � � � 3
National and regional training on biodiversity
informatics in Argentina, Africa and Asia

NEW DATA� � � � � � � � � � � � � � � � � � 4
Finland
NorwaySwedenUnited Kingdom
IrelandUnited States
CanadaUPCOMING EVENTS � � � � � � � � 5

The GBIF Finland node manager, Hannu Saarenmaa, said:“Digitarium came to the conclusion that traditional, manual
work will not cut it in digitizing those millions of specimensin the world’s collections.
“It seems to be plausible to run 1000 samples throughour system in one working day with a workforce of one tothree people. This will be achieved by automated conveyor
belts, sensors, image pattern recognition in real time, andintelligent software.”A demonstration of the system will take place at a miniworkshop organized by Digitarium in Joensuu on 29
October. If you would like to attend, please contact
hannu.saarenmaa@uef.fi.
Read more…

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

GBits
GBIF PUBLICATIONSSCIENCE AND POLICY

New guide for developing marine species
checklists

Fourth GBits Science Supplement
published

GBIF has published a new guide highlighting someof the procedures and online resources to help build
and maintain species checklists for marine regions.

As usual, recent uses of biodiversity data discovered
and accessed through the GBIF network aresummarized in the companion publication to thisnewsletter, the GBits Science Supplement. Issue
Four of the supplement, covering August and theearly part of September 2012, highlights research onpresent and potential future distribution of vampirebats; on the plant content of traditional aphrodisiac
mixtures used in Afro-Caribbean and West African
cultures; and the potential spread of the invasive
Australian windmill grass (Chloris truncata).

The publication, Best Practice Guidelines in theDevelopment and Maintenance of Regional Marine
Species Checklists, outlines the steps required tocompile distribution notes, to set up a register, andto produce a checklist. It also describes some ofstumbling blocks that might be encountered along
the way, and offers suggestions on how to overcomethem.
The publication was developed for GBIF by its marinebiodiversity partners: the Ocean Biogeographic
Information Systems (OBIS), the World Registerof Marine Species (WoRMS) and Fisheries andOceans Canada. It complements other recent GBIF
publications on developing species checklists andtaxonomic names, all available through the GBIF
Online Resource Centre.
Read more…

TAXONOMY
Naming of animal species moves into thedigital age
A landmark decision by the body that regulates
zoological names has ended the centuries-old rulethat new animal species must be described in a
printed journal.
After a highly-charged debate among taxonomists
lasting four years, the International Commission
on Zoological Nomenclature (ICZN) has passed
an amendment to its code, allowing electronic
publication of new names, under certain conditions.
The amendment, published simultaneously inZookeys and Zootaxa journals, changes the codeto accept electronic-only publishing as ‘legitimate’if it meets criteria of archiving and the publicationis registered at the ICZN’s official online registry,
Zoobank.
Read text of amendment here…
Read ICZN press release here …

22AROUND THE NETWORK
Digital catalogue of New Zealand’sbiodiversity launched
The New Zealand Organisms Register (NZOR) waslaunched in August. NZOR is the national digitalspecies catalogue for New Zealand and contains
fundamental information on taxonomic names,synonyms, classification, nomenclatural data,
common names and bibliographic data for around70,000 organisms, indigenous or introduced (in thewild or in captivity) to New Zealand.
NZOR is based on a federated data network ofnational taxonomic data providers which includes thenational plant, fungi and animal collections, together
with data from the recently-published New Zealand
Inventory of Biodiversity. The NZOR infrastructuredelivers a set of web services to facilitate data
discovery, access and integration into end-user data
management systems supporting the New Zealandconservation, biosecurity and environmental researchsectors.
For further information, please contact Jerry Cooper,
NZOR Project Manager and NZ GBIF Node Manager(cooperj@landcareresearch.co.nz) or Kevin Richards,
NZOR Developer (richardsk@landcareresearch.co.nz),
Landcare Research, New Zealand.

Atlas of Living Australia develops tests todetect suspect records and duplicates
The Atlas of Living Australia (ALA) has implemented a
set of tests to identify suspect records automatically.
The ALA, which hosts the GBIF national node inAustralia, runs an algorithm known as Reverse
JackKnife to find spatial outliers, records that arousesuspicion because they fall significantly outside therange suggested by the rest of the data.

Aug 2011

A discussion on the algorithm used is at http://code.
google.com/p/ala-dataquality/wiki/DETECTED_OUTLIER_JACKKNIFE.
The ALA has also developed tests to find duplicate
records. One method will be to flag specimensthat were collected by the same person as part ofthe same collecting event. For observations, thesystem may flag duplicate observation records thathave historically been shared between datasets.
Identification of this kind of duplicate is of particularinterest for distribution modelling.
Technical implementation of the tests is discussed
here (for outliers) and here (for duplicates).

Ireland’s biodiversity data centre appeals
for insect records
GBIF’s partners in Ireland are appealing for help
from the public to develop an atlas of grasshoppers,
crickets and earwigs.
The National Biodiversity Data Centre (NBDC) is
collaborating with the United Kingdom’s Biological
Records Centre to map the distribution of these insectgroups in the UK and Ireland.
To help with observations from citizens, NBDC has
issued identification guides for the target species.

no 30 Sep 2012

Stephen Hopper made his comments to the Guardian
newspaper shortly before completing his six-year
term as chief executive of Kew, which publishes morethan half a million specimen records to the GBIF
network.
“We’re at a crossroads in many ways, we now have
half the remaining wild vegetation on the planet leftthat was around 200-300 years ago,” said Hopper.
“One-third of the plant species we looked at, wedidn’t have enough data,” said Hopper. “Of thetwo-thirds for which we did have data, one-fifth ofthem were threatened in some way. We finally havereasonable statistics at a global level to understandthe scale of the problem and it’s formidable. Some
80,000 species on the planet are at some risk of going
extinct over the next 50-100 years,” said Hopper.
Read the full interview in the Guardian….

TRAINING
National and regional training on
biodiversity informatics in Argentina,
Africa and Asia

A national workshop on data quality andmanagement for natural history collections inArgentina gathered 37 participants from institutions
all over the country, from 3-7 September.
Topics at the workshop ranged from data capture andlabels to linking collections to molecular datasets andthe semantic web.
Francisco Pando and Katia Cezón from GBIF Spain
were instructors. The event was organized by theCentro Nacional Patagónico (CENPAT), a research
centre under the Argentinian government agency on
scientific research – CONICET. Support was provided
by the National System for Biological Data SNDB, an
initiative of the Argentinian Ministry of Science.

Common earwig (Forficula auricularia)

Read more…

Records may be submitted at iti.ms/Pyzp6n.

The Albertine Rift Conservation Society (ARCOS),an Associate Participant of GBIF, organized a threeday training event in Kigali, Rwanda, on building
biodiversity information systems in the region.

The story was carried in the Irish Times under theheadline ‘Bugged by the hugely under-recorded
presence of earwigs’….

‘New deal’ needed for world’s plants –outgoing Kew director
People around the world need to embrace a‘new deal’ to recognize the economic, health andenvironmental benefits of plants, according to theoutgoing director of Royal Botanic Gardens, Kew, inLondon.

Staff from various data-holding institutions in theAlbertine Rift region – Uganda, the Democratic
Republic of Congo (DRC), Rwanda, Burundi andTanzania – were trained in Geographic Information
Systems (GIS), remote sensing and databasemanagement systems.
Participants at the event, from 3-5 September, wereled through the steps of uploading and publishingdata to the regional biodiversity portal, which is under33GBitsdevelopment. The Tanzanian biodiversity information
facility TanBIF facilitated some sessions on the GBIF
Integrated Publishing Toolkit (IPT).
The project to share biodiversity information in theregion is funded by the JRS Biodiversity Foundation.
The JRS Biodiversity Foundation is also fundinga three-year programme to build biodiversity
informatics capacity in Africa. A. Townsend Peterson,
professor of ecology and evolutionary biology at
the University of Kansas, will lead multiple training
sessions in four African nations: Ghana, South Africa,
Kenya and Egypt. A global online training curriculum
for biodiversity informatics will be developed throughthe programme. Activities related to this project
can be followed on the facebook page https://www.
facebook.com/groups/BiodiversityInformatics/.
The first course is to be held in Nairobi, Kenya, from25-28 February 2013, on ecological niche modelling.
A two-day training event on biodiversity data
publishing in the Hindu Kush Himalayan region wasorganized by the International Centre for Integrated
Mountain Development (ICIMOD), a GBIF Associate
Participant, in Kathmandu, Nepal, from 23-24 August.
Twenty-two participants were trained in data
publishing, platforms for data sharing and in using
the IPT. The participants represented governmentorganizations, universities, research institutes
and NGOs from eight ICIMOD member countries– Afghanistan, Bangladesh, Bhutan, China, India,Myanmar, Nepal and Pakistan.
The event was one of the four regional training
proposals to receive GBIF funding support in 2012.

NEW DATA

NorwayOver eight million records from Norway werepublished to the GBIF network in August. The majorityof the data records were from citizen science reports
of fish, birds, mammals, plants and insects in thecountry. Other new datasets included: records ofvascular plants in the Arctic archipelago of Svalbard;
insects from the Stavanger Museum collections;the butterfly, horsefly and spider collections of theHelgeland Museum; and snails and slugs from theBergen Museum.
(http://data.gbif.org/datasets/resource/14377,
http://data.gbif.org/datasets/resource/14380,
http://data.gbif.org/datasets/resource/14381)

SwedenThe Gothenburg Natural History Museum has
published 48,600 records of invertebrates and 55,800
records of vertebrates from its collections. The
museum’s holdings include rare items like the skin of
the Tasmanian Wolf, extinct since 1933, specimens of
the extinct Passenger Pigeon, and a sub-fossil skeletonof the Great Auk. The museum’s collection of fishfrom Sweden dates back to the 1840s and it hosts thelargest Swedish collection of parasitic worms.
(http://data.gbif.org/datasets/resource/14391,
http://data.gbif.org/datasets/resource/14384)

United Kingdom
The UK Environment Agency has published about
37,000 records collected through surveys andmonitoring of invertebrates, plants, algae and fish.
Rare and protected species such as the Whiteclawed crayfish (Austropotamobius pallipes) the only
species of crayfish native to the British Isles, and theEuropean eel (Anguilla Anguilla) are included in thedataset.
(http://data.gbif.org/datasets/resource/14389)

Finland
The Finnish Museum of Natural History has publishedclose to 900,000 records from its winter bird census,
which dates back to 1956. Data come from volunteer
birdwatchers who monitor wintering birds in Finland.
During the winter of 2011/2012, data were collected
via the Internet for the first time.
Volunteers taking part in the census freely design
their own route of 5-15 kilometres, which they
monitor three times during the winter. The idea isto monitor all bird species listed, including missing
species. Reports are then sent to the coordinatingteam and records are categorized by habitats andregistered. These winter bird surveys are especiallyhelpful in monitoring increase or decrease of common
bird species.
(http://data.gbif.org/datasets/resource/14354)
44White-clawed crayfish (Austropotamobius pallipes)

Aug 2011

Ireland

193,000 records of moths from Ireland have been
published by the National Biodiversity Data Centre.
Most of the records are from light traps and are aimed
at providing a distribution map of moth species. Over1350 moth species have been recorded, of whichmore than 570 are macro-moth (i.e. larger) species.
(http://data.gbif.org/datasets/resource/14385)

United States
The Field Museum of Natural History in Chicago has
published over 1.2 million records of specimens fromboth the animal and plant kingdoms. The museum’s
fish and mammal collection dates back to the 1890’s,
and it houses the third largest collection of birds inthe country.
The museum has one of the largest mammalcollections in the world and has some of thebest holdings from the Philippines, Peru, Chile,Madagascar, Tanzania, Egypt, and Iran.
(http://data.gbif.org/datasets/provider/49)
The California Academy of Sciences has publishedclose to 200,000 records from its insect collection.
Among the significant areas represented in thedataset are Madagascar, São Tomé and Príncipe andthe China-Burma border area.
(http://data.gbif.org/datasets/resource/14364)
A number of new datasets have been published
via the GBIF Integrated Publishing Toolkit (IPT)
installed by VertNet, the global network of vertebratecollection data. They include about 30,000 vertebrate
records from the Charles R. Conner Museum based atWashington State University; 219, 000 records fromthe Texas Cooperative Wildlife Collection, a natural
history collection maintained by the Texas A&M
University; 18,700 records from the avian holdingsof the Cowan Tetrapod Collection located in British
Columbia, Canada; and 31,500 records of vertebrates
from the collections of the University of Texas at El
Paso.
(http://data.gbif.org/datasets/resource/14363,
http://data.gbif.org/datasets/resource/14379,
http://data.gbif.org/datasets/resource/14386,
http://data.gbif.org/datasets/resource/14396)

no 30 Sep 2012

CanadaTwo more datasets have been published throughthe GBIF Integrated Publishing Toolkit (IPT) hostedby the Canadensys data repository. The Louis-MarieHerbarium, based at the Laval University in Québec
published 66,000 records of vascular plants from its
collection of Arctic-alpine, subarctic and boreal plant
species from Canada and the northern hemisphere.
The University of British Columbia Herbarium
published 22,000 records of fungi, which account for
95% of its collection.
(http://data.gbif.org/datasets/resource/14361,
http://data.gbif.org/datasets/resource/14362)

UPCOMING EVENTS
14th Annual BIOECON Conference - Resource
Economics, Biodiversity Conservation andDevelopment
18-20 September 2012, Kings College, Cambridge,
United Kingdom
More information…
19th meeting of the GBIF Governing Board (GB19)
and Science Symposium
16-21 September 2012, Lillehammer, Norway
More information…
Biodiversity Technologies Symposium
27-28 September 2012, University of Oxford, United
KingdomMore information…
PersistentIDs workshop
3 October 2012, Université Libre de Bruxelles,
Brussels, Belgium
More information…
11th meeting of the Conference of the Parties to theConvention on Biological Diversity (CBD COP 11)
8-19 October 2012, Hyderabad, India
More information…
2012 Biodiversity Information Standards (TDWG)
annual conference
22-26 October 2012, Beijing, China
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 ØDenmark

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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