Providing and using (open) biodiversity data through the infrastructure of the Global Biodiversity Information Facility
(GBIF): lessons and achievements of the first 10 years
Cees H.J. Hof
Netherlands Biodiversity Information Facility (NLBIF)
The Dutch branch of the Global Biodiversity Information Facility (GBIF)
"Biological diversity" means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems….
What is biodiversity?
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Biodiversity data are….
Natural history collections
Living collections
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Biodiversity data are….
Citizen science data
Systematic monitoring + research data
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Biodiversity data for:Taxonomy
Biomimicry studiesEducation and public outreachBorder control and wildlife tradeForensics
Health and public safetyAgriculture, forestry, fishing and mining
Natural resource managementConservation planning
Ecology, evolution and genetics
Impact of climate change
Endangered, migratory and invasive species
Life histories and phenologiesSpecies diversity and populations
Biogeographic studies
Fundamentalresearch
AppliedresearchEcotourism
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Biodiversity data for:Taxonomy
Biomimicry studiesEducation and public outreachBorder control and wildlife tradeForensics
Health and public safetyAgriculture, forestry, fishing and mining
Natural resource managementConservation planning
Ecology, evolution and genetics
Impact of climate change
Endangered, migratory and invasive species
Life histories and phenologiesSpecies diversity and populations
Biogeographic studies
Fundamentalresearch
AppliedresearchEcotourism
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
The mission of the Global Biodiversity Information Facility (GBIF) is to facilitate free and open access to biodiversity data worldwide via the Internet to underpin sustainable development.
Megascience Forum Working Group on Biological Informatics
1999 The purpose of GBIF is to co-ordinate the standardisation, digitisation and global dissemination (within an appropriate property rights framework) of the world's biodiversity data.
Ministers acknowledged the importance of such a facility in the areas of health, resource management, environmental protection, agriculture and education.
2001 GBIF established and secretariat settled in Copenhagen
History of GBIF
Founded by OCW, NWO and UvA2002NLBIF
2012 Currently structurally financed by OCW, hosted by UvA
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
The mission of the Global Biodiversity Information Facility (GBIF) is to facilitate free and open access to biodiversity data worldwide via the Internet to underpin sustainable development.
Mobilising biodiversity data, developing protocols and standards to ensure scientific integrity and interoperability, building an informatics architecture to allow the interlinking of diverse data types from disparate sources
Distributed network, both technical and organisational
Focus on species occurrence data and metadata, but expanding to new data types
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
GBIF country participants
Data published through GBIF.orgTrend in primary biodiversity records (millions)
Jan-
08Ma
r-08
May-0
8Ju
l-08
Sep-
08No
v-08
Jan-
09Ma
r-09
May-0
9Ju
l-09
Sep0
9No
v-09
Jan-
10Ma
r-10
May-1
0Ju
l-10
Sep-
10No
v-10
Jan-
11Ma
r-11
May-1
1Ju
l-11
Sep-
11No
v-11
Jan-
12Ma
r-12
May-1
2Ju
l-12
Sep-
12No
v-12
Jan-
13Ma
r-13
May-1
3Ju
l-13
Sep-
13No
v-13
Jan-
14Ma
r-14
May-1
4Ju
l-14
Sep-
14No
v-14
Jan-
15Ma
r-15
May-1
5Ju
l-15
Sep-
15
200
250
300
350
400
450
500
550
600
650
700
750
800
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Data by gbif participant
1. United States 212,958,707 6. Netherlands 27,503,881
2. Sweden 52,601,060 7. Finland 20,157,055
3. United Kingdom 49,616,634 8. Germany 19,221,758
4. Australia 40,373,693 9. Norway 19,140,600
5. France 39,619,893 10. Spain 10,667,845
Total number of records published—Top 10 Participant Countries (as of 30 September 2015)
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
The primary GBIF data:What is a record in GBIF?
GBIF hosts so called “occurrence data”
Which species of plant / animal / micro-organism was observed / collected from which locality and when?
Taxonomic information Geographic information
01 May 197100:00:00
Temporal information
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
http://www.gbif.org/occurrence
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
http://www.gbif.org/species
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Search for:
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Find….Filter ….& Download
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Central data portal
Centraldata index
Distributed data publishers
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
API’s
The GBIF infrastructure
The two success formulas driving GBIF:
The datastandard for biological data: Darwin Core (DwC)
Body of data standards which function as an extension of Dublin Core for biodiversity informatics
9 categories, about 180 terms
Additional info in data extensions, data zipped in “Archives”
The Integrated Publishing Toolkit (IPT)
An easy to deploy toolkit to “publish” your primary biodiversity data and your metadata
Free and open source, based on the efforts of a community
Provided with standard CC licencing options + using DOI’s
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
The GBIF data model(DarwinCore-Archives)
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Handles multiple datasets
Feed spreadsheets, CSV files or connect to your institutes database
For primary data + metadata
The GBIF Integrated Publishing Toolkit (IPT)
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Using Creative Commons
Using DOI’s
Worldwide:
In NL: NIOZ, IBED (UvA), Alterra (WUR), CGN (WUR), Naturalis, NLBIFSovon, RAVON, Floron
Installations of the Integrated Publishing Toolkit (IPT)
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Use of GBIF data in research….
Annual number of peer-reviewed publications using GBIF-mediated data
2008
2009
2010
2011
2012
2013
2014
2015 (Jan-Sep)
0 50 100 150 200 250 300 350 400
52
89
148
169
229
249
357
293
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
GBIF data download requests, by country
1. Mexico 13,589 6. Colombia 3,202
2. United States 9,165 7. United Kingdom 2,920
3. China 5,294 8. South Africa 2,170
4. Brazil 5,109 9. Australia 1,950
5. Spain 3,785 10. Ecuador 1,824
Total of 73,719 requests
from 6,833 users in
140 countries, islands and territories
1 Jan 2015 – 30 September 2015
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
(Billion records per day!)
Use of the GBIF infrastructure at the national level….
WUR E-depot
Paper
Dataset
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Use of the GBIF infrastructure at the national level: feeding metadata to NARCIS
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Use of the GBIF infrastructure at the national level: providing “GBIF views” on EASY data
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
GBIF lessons…
Start simple
Distributed data systems, distributed applications(strong, cheap, resilient, …..)
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015
Agile developments, continuing interaction with users
Thematic interaction with research community
http://www.gbif.org
http://www.nlbif.nl
THANK YOU!
Cees HofNetherlands Biodiversity Information Facility (NLBIF) Connecting data for research 2015