GBits

no. 39 Mar 2014

DATA PUBLISHING � � � � � � � � � � 2free and open access to biodiversity data

New features introducedin GBIF Portal

Occurrence records accessible through GBIF now present
richer information following the release of a new version of
the GBIF portal.
Users of the portal can access many more fields ofinformation in the detailed occurrence record pages. Thishas been made possible thanks to the new distributed
technologies recently adopted by GBIF, allowing use ofmultiple servers.
Previous versions of the portal displayed only about 30 of
the 150 terms from the Darwin Core standard, whereas
visitors to the portal can now access other details madeavailable by the publisher. These include information suchas sampling methodology, collectors’ names and fieldnotes.
As an example, an occurrence record of a Plum fruited
yew published by the Royal Botanic Garden in Edinburgh,provides in-depth notes of the habitat in which the plant
was collected in Chile. Another page related to a record ofa lichen specimen from a Kansas herbarium includes therecorders’ names and information about the soil conditions
and other information on the location where the specimen
was collected.
Downloads of these newly ‘widened’ occurrences containall published information on each of the records.
A much-requested feature over the past year has been theability to search occurrences by type status. Types referto physical specimens kept in a museum or herbarium towhich the name of that organism is formally attached. This
information is therefore of critical importance to taxonomic
researchers. The filter is now available on the occurrence
search page, and allows queries such as the records
designated as a Holotype.

Real-time data publication from taxonomic
research
First data paper from Portugal published

NEW DATA � � � � � � � � � � � � � � � � � � 2Benin
Chinese Taipei
Czech Republic
The Netherlands
Spain
FranceGermany
Colombia
United States
CanadaPensoft Publishers

AROUND THE NETWORK � � � � 3
TraitBank launched
OpenUp! mobilizes 1.6 million multimedia objects
White paper on genome data portal publishedWorkshop on the new GBIF portal held in Spain

OPPORTUNITIES � � � � � � � � � � � � 4
New appointments to enhance GBIF data contentand use
Nominations invited for 2014 GBIF science awards

EVENTS � � � � � � � � � � � � � � � � � � � � 5Meetings and conferences
Training courses

The release is the first of a two-stage process to improveinformation available via the GBIF portal. The next releaseof the portal in the coming weeks will enable users to view
images, and access audio and video files associated withoccurrence records.

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

GBitsDATA PUBLISHING
Real-time data publication fromtaxonomic research

Researchers and the public can now have immediateaccess to data underlying discovery of new species oflife on Earth, under a new streamlined system linking
taxonomic research with open data publication
through GBIF and other networks.
The partnership involving Pensoft Publishers paves
the way for unlocking and preserving a wealth of‘small data’ backing up research conclusions, which
often become lost within a few years of an article’s
publication in an academic journal.
In the first example of the new collaboration inaction, the Biodiversity Data Journal carried a peerreviewed description of a new species of spider Crassignatha danaugirangensis - discovered during
a field course in Borneo just one month earlier anddescribed via satellite from the field. As soon as
the journal published the paper, data showing thelocation of the spider’s occurrence in nature wereautomatically harvested by GBIF, and richer data suchas images and the species description were exported
to the Encyclopedia of Life (EOL).

GBIF Benin also published 1000 records from tree
inventories in the Bonou and Itchèdè and Pobè
forests in the south east of the country. Bothinventories were carried out to gather information forthe sustainable management of the forests.

Chinese Taipei
Over 100,000 records of plant specimens from theisland of Taiwan have been published via the GBIF
portal. The dataset, with records dating back to 1895,
includes endemic species such as Gentiana scabrida
Hayata, Cycas taitungensis, Begonia chitoensis andGastrochilus fuscopunctatus. Data are from thecollections of the herbarium at the National Taiwan
University, which holds representative specimensof about 95 per cent of species of vascular plants inTaiwan. Most of the collection of 260,000 specimens
has been digitized.

Read full story…

First data paper from Portugal published
Researchers from Portugal have published thecountry’s first data paper based on a biologicalcollection shared via GBIF. The article in Zookeys
by Miguel Monteiro and colleagues describes acollection of birds of Angola at the Instituto deInvestigação Científica Tropical in Lisbon, host of
the national GBIF node. The institute houses 1560
bird specimens of 161 species and 361 subspecies,
including threatened species such as the wattled
crane (Grus carunculata) and the Gabela bush-shrike(Laniarius amboimensis).

Gentiana scabrida Hayata. By Chun-Kuei Liao. CC-BY-NC.

Czech Republic

A data paper is a searchable metadata document,describing a particular dataset or a group of datasets,published in the form of a peer-reviewed article in ascholarly journal.

The National Museum in Prague has become thefirst institution in the Czech Republic to publish
datasets through GBIF. The 56,300 records relate to
the museum’s botanical, entomological, mycological,zoological and paleontological collections. The Czech
Republic is not yet a national Participant in GBIF, andthe museum was endorsed as a data publisher by
the Consortium for European Taxonomic Facilities.
The collections have been mobilized through theBiological Collection Access Service for Europe.

NEW DATAThe Netherlands

Benin
GBIF Benin has published over 10,000 records from a
census of the country’s plants. The dataset includes
species that are of cultural and economic importance,such as the Wild syringa (Burkea Africana),
Anogeissus leiocarpa, one of the plants used tomake traditional Malian mudcloth, and Pterocarpus
erinaceus, used for medicinal purposes.

22

The City of Amsterdam has published 8,900 records
from an urban fish monitoring project in the city’s
harbor area. The survey of fish biodiversity wascarried out by commercial eel fisherman Piet Ruijter,
who has been fishing in the city’s waters since hewas 15. For the survey, Ruijter used fyke nets – bagshaped nets held open by hoops, typically used tocatch eels.

Aug 2011

Spain

The Botanical Garden of Barcelona, has publishednearly 3,000 records from its seedbank, built toact as a reference centre for the conservation ofMediterranean flora. Most of the data come fromSouthern Europe, North Africa and the Middle East,with some additional records from Australia, Chile,
the United States and South Africa.
Also from Barcelona is a dataset published by theNatural History museum with observation recordsof terrestrial molluscs from the Natural Park of theSerralada Litoral, a range of mountains runningparallel to the Mediterranean Sea in Catalonia. Data
were gathered during an assessment in the area todevelop a conservation plan.

no 39 Mar 2014

Colombia

The International Center for Tropical Agriculture
has published 1,500 records of herbivorous mites,
documented by the organization between 1975 and2012.
Some species of the Mononychellus genus are pests
which affect cassava, a staple food crop in many partsof the tropics. The dataset comprises observationaland specimen-based occurrence data and most of
the records are from the genus’ native range in SouthAmerica, with other records from six countries inCentral America, four in Africa and two in Asia.

The herbarium at the University of León innorthwestern Spain has published 9,000 records oflichens, collected by researchers in the northern partof the Iberian peninsula.

The Alexander von Humboldt Institute has published
2,700 records of the flora and fauna of the páramo, atype of alpine tundra ecosystem unique to the Southand Central America. The data were gathered in themunicipality of Sotará in southwestern Colombia, aspart of a project to map biodiverse areas that are notprotected.

FranceUnited States

The Institut National de la Recherche Agronomique(INRA), has published two datasets related toagricultural research.

The Museum of Biological Diversity at the Ohio State
University has published 42,700 observation records
from sound recordings of birds, animals and insects
gathered by the Borror Laboratory of Bioacoustics.
The lab holds one of the largest animal sound archives
in the world.

INRA holds a major collection of the Medicago genus,
a legume native to the Mediterranean region. One ofthe datasets consists primarily of specimen records
for Medicago truncatula or barrel clover , a species
used in genomic research, as well as for two otherspecies - Medicago littoralis and Medicago tornata.
The second dataset relates to young potato plants(Solanum tuberosum) that are maintained in test
tubes by INRA or as field-produced tubers, and areavailable as genetic resource material. These living
specimens come from old cultivars of potato thatwere grown in France in the past, and were collectedby scientists at INRA and breeders from French seedcompanies.
Among other data published from France are anumber of historically-important records, including
two datasets from the Henri-Lecoq museum inClermont Ferrand, central France. One includes
specimens of the rose family (Rosaceae) collected
between 1790 and 1913. The other dataset consists ofrecords of freshwater molluscs, collected in the mid19th century. The Zoological Museum of Strasbourg
has also published data records of sponges collectedin the 19th century.

GermanyThe Leibniz Institute DSMZ has published 6,900
records of myxobacteria, a group of organisms
which live in the soil and feed on insoluble organic
substances. The institute’s collection comprises about
7,000 strains of the bacteria.

CanadaThe University of Alberta Vascular Plant Herbarium
has published 69,000 records, relating to over half
the specimens held in the herbarium. The publisheddata are from around the world with an emphasis onAlberta and the western Arctic.

Pensoft Publishers
Data records from an analysis of 17 species of theMegophthalmidia genus of flies in North America,
including eight new species, are now available via
GBIF. The species are described in a paper publishedin the peer-reviewed open access journal ZooKeys.
The Megophthalmidia genus belongs to theMycetophilidae family, made up of mainly fungus
gnats, so named because their larvae feed on plantroots and fungi and aid in their decomposition.

AROUND THE NETWORK
TraitBank launched
The Encyclopedia of Life (EOL) has launched a newservice called TraitBank, a searchable repository
for traits, measurements, interactions and otherattributes associated with the species included within33

GBits
EOL’s database. The site features over three million
records relating to more than 250 attributes recordedfor 272,000 taxa.
Read more…

OpenUp! mobilizes 1.6 million
multimedia objects
The EU-project OpenUp! has mobilized and madeavailable over 1.6 million multimedia objects
relating to natural history in the three years since
its inception. The objects are accessible through theEuropean digital library Europeana, based on BioCASeand GBIF tools. The data mobilized puts the project
among the top ten content providers to Europeana.

White paper on genome data portal
publishedA white paper on the Global Genome Biodiversity
Network (GGBN) has been published.
GBIF is a partner of the GGBN, which was formed
in 2011 with the principal aim of making highquality well-documented and vouchered collections
that store DNA or tissue samples of biodiversity,
discoverable for research through a networked
community of biodiversity repositories. This isachieved through the GGBN Data Portal, which links
globally distributed databases and bridges the gap
between biodiversity repositories (natural history
collections, tissue banks, DNA banks and culturecollections), sequence databases and research results.
All underlying specimen data are also published viaGBIF.

Workshop on the new GBIF portal held in
Spain
GBIF Spain presented the functionalities of the new
GBIF portal in a workshop organized on 5 March 2014.
The features highlighted included greater visibility
for countries and institutions sharing data, improved
search and mapping, showing information about
database activity and statistics, unlimited downloads,
real time indexing and building searches using
web services. Special emphasis was placed on thepossibilities provided by the APIs.

A special feature is the common names service, whichadds vernacular names in more than 27 languages
to the scientific objects. This metadata enrichmentservice greatly improves the semantic linking ofnatural history content with other domains andfacilitates easy access to the collections.
OpenUp! held its third and final annual meetingin Bratislava on 20-21 February this year, with asymposium entitled Collections in the virtual world,
and a workshop on intellectual property right issues
based on the OpenUp! document IPR problems andsolutions for the domain of natural history objects.
OpenUp! is a three-year project running from 2011
to 2014, and is an initiative of members of theConsortium of European Taxonomic Facilities (CETAF)
and several European GBIF nodes. The consortium
believes it will continue to provide multimedia
content to Europeana.

44Sixteen people attended the event and about ahundred more followed it via live streaming. Remoteparticipants could submit questions in real time via
Twitter.
Videos from the event are available through GBIF
Spain’s website.

OPPORTUNITIESNew appointments to enhance GBIF data
content and use
The GBIF Secretariat invites applications for two staff
positions focussed on enhancing the biodiversity data
available through the network, and supporting theuse of data in research and policy. The vacancies arefor a Programme Office for Content Mobilisation, andfor a Programme Officer for Content Analysis and Use.
The deadline for applications is 22 April.
More details…

Aug 2011

Nominations invited for 2014 GBIF
science awards
GBIF invites nominations for the 2014 Ebbe Nielsen
Prize and Young Researchers Awards.

no 39 Mar 2014

EVENTS
Meetings and conferences
Open Repositories Conference
9-13 June 2014, Helsinki, FinlandMore information…

The Ebbe Nielsen Prize has been awarded annuallyto a person or team who demonstrates excellence in
combining biodiversity informatics and biosystematics Atlas of Living Australia Science Symposium
research. The €30,000 award is intended to allow the 11-12 June 2014, Canberra, Australia
recipient(s) to engage in biosystematics/biodiversity
More information…
informatics research outside his/her/their country ofresidence for a period of 3-6 months.
Training courses
The Young Researchers Awards intend to foster
Introduction to individual based models in ecology
innovative research and discovery in biodiversity
using NetLogo by Transmitting Scienceinformatics. Two awards of €4,000 will be available
26-30 May 2014, Els Hostalets de Pierola, Spainto graduate students in a master’s or doctoral
More information…
programme at a university in a GBIF Voting Participant
or Associate Participant country.
I3B Workshop: Foundations, evaluation and future ofthe species distribution models
Nominations for the 2014 Ebbe Nielsen Prize and the 2-6 June 2014, Tepoztlán, Mexico
2014 Young Researchers Awards are due on 31 May
More information…
2014.
More details…

VISION OF GBIF: A world in which biodiversity
information is freely and universally available forscience, society, and a sustainable future.
GBIF Secretariat
Universitetsparken 15
DK-2100 Copenhagen ØDenmark
http://www.gbif.org/MISSION OF GBIF: To be the foremost global
resource for biodiversity information, and engendersmart solutions for environmental and human wellbeing.
Tel: +45 35 32 14 70
Fax: +45 35 32 14 80
E-mail: info@gbif.org
GBits archive: http://www.gbif.org/newsroom/
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