Intro to GBIF: Infrastructures and Platforms for Environmental Crowd Sensing and Big Data
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9 SEPT 2015 EnviroInfo & ICT4S 2015 Kyle Copas
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Transcript of Intro to GBIF: Infrastructures and Platforms for Environmental Crowd Sensing and Big Data
9 SEPT 2015
EnviroInfo & ICT4S 2015Kyle Copas
WHAT IS GBIF?
http://www.gbif.org
• Open-access research infrastructure for biodiversity information, funded by the world’s governments
• Established in 2001 on recommendation byOECD Global Science Forum in 1999
• 92 national and organizational participants: ‘member state’ approach
• Secretariat hosted by KU and attached to the Zoological Museum in Copenhagen
WHAT DOES GBIF DO?
• Provides and maintains open access and web services to global species data through GBIF.org
• Promotes common standards and free tools for biodiversity data management and exchange
• Offers guidance on national mobilization of biodiversity information
• Supports collaborative network at global and regional levels
www.gbif.org
GBIF BY THE NUMBERS
570,330,659 species occurrence records
1,611,321 species
15,109 datasets
763data-publishing institutions
http://www.gbif.org | 9 SEP 2015
CITATIONS IN PEER-REVIEWED RESEARCH
2 SEP 2015
rese
arch
use
Annual number of peer-reviewed publications using GBIF-mediated data
2008
2009
2010
2011
2012
2013
2014
2015 (Jan-Aug)
0 50 100 150 200 250 300 350 400
52
89
148
169
229
249
357
261
OCCURRENCE DATA SHARED THROUGH GBIF
Observations from field surveys,
inventories and citizen scientists
Records extracted from literature
Specimens from museum and
herbarium collections
DARWIN CORE ARCHIVE (DwC-A)
http://rs.tdwg.org/dwc/terms/guides/text/index.htm
DARWIN CORE ARCHIVE (DwC-A)
http://rs.tdwg.org/dwc/terms/guides/text/index.htm
Preferred format for publishing data to GBIF• Simple format: text files• Efficient harvesting: single file• Efficient storage: compressed• Easy access: no special software required• Extensible: related files in one archive
http://www.gbif.org/newsroom/news/sample-based-data
• Darwin Core extension for sample-based data ratified by TDWG
• IPT v2.3 (released today?) supports publication of sample-based datasets
• Training manual on publishing sample-based datasets coming in Oct 2015
• GBIF.org to add simple search and discovery of sample-based datasets in 2016
data mobilization
SAMPLE-BASED DATA2015 objective: Enable mobilization and discovery of biodiversity
monitoring data using defined sampling protocols, including measures of species abundance
Photo CC BY-ND 2014 Florida Fish and Wildlife, Karen Parker https://flic.kr/p/pJVe2R
DwC-A WITH EVENT CORE
http://rs.tdwg.org/dwc/terms/guides/text/index.htm
Event core
Occurrence
Measurement-or-fact
…
meta.xml
EML.xml…
+DwC Archive
…
GBIF API v1
RESTful JSON-based API provides discovery, access and information services to users (including GBIF) for
• Registry: administrative details• Checklists: taxonomies and spp. info• Occurrences: search and download• Maps• Metrics and utilities
Active, responsive mailing list for API usersFully documented on GBIF.org
http://www.gbif.org/developer/summary
REPORTING ON DATA TRENDS
http://www.gbif.org/analytics/global
glob
al
REPORTING ON DATA TRENDS
http://www.gbif.org/analytics/country/SE/published
swed
en
http://www.gbif.org/country
• Currently connecting data and other APIs to automate national reporting
• Intended to show important details on national use and impact of GBIF
• Links metrics, trend analysis and recent content
• Board review of prototype reports next month; roll-out expected for all countries in early 2016
wnat’s next
COUNTRY REPORTS2015 objective: Provide regular updates to highlight availability, use and
impact of data mobilized by the GBIF network at national level
GBIF API: JSON RESPONSE
http://api.gbif.org/v1/occurrence/985492326/fragment
DATA SOURCES
Citizen science networks• eBird: 150 million high-quality
observations• Recorder networks in UK,
Sweden, Norway, Finland et al.Bioblitzes• Sometimes hosted by national
and organizational participants• Important tool for public outreach
Crowdsourced digitization• Virtual public transcription
projects: ongoing or timebound
citiz
en s
cien
ce
CITIZEN SCIENCE DATA: 2014TOP NATIONAL PUBLISHERS EXCLUDING eBIRD
GBIF Secretariat analysis, Nov 2014
Country # ObservationsUSA 161,894,332Sweden 38,604,747UK 22,304,967Finland 13,519,114Australia 7,448,478Germany 4,951,803Denmark 4,609,679Ireland 1,582,524Norway 370,911Estonia 169,086Belgium 370,911Canada 121,916
Country # ObservationsSweden 38,604,747UK 22,304,967Finland 13,519,114USA 8,362,169Australia 7,448,478Germany 4,951,803Denmark 4,609,679Ireland 1,582,524Norway 370,911Estonia 169,086Belgium 370,911Canada 121,916
citiz
en s
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BASIS OF RECORD
• Greater proportion of observations
• Contributions to specimen data are underreported and underappreciated
GBIF Secretariat analysis, Nov 2014
Basis of record Citizen science Institutional
Human observation 204,330,760 67,405,200
Observation 45,803,179 55,760,093
Unknown 3,782,583 36,026,607
Preserved specimen 1,984,634 97,090,284
Literature 51,204 404,875
No information 81 3
Fossil specimen 47 3,850,597
Living specimen 0 822,136
Machine observation 0 689,739
Material sample 0 2,293
Ratio of specimens 0.8% 39%
citiz
en s
cien
ce
CITIZEN SCIENCE NETWORKS
iNaturalist• Naturalists + social media +
photo sharing = citizen science
• Open source software leveraging existing APIs
• Community curation produces ‘research grade’ observations
http://www.inaturalist.org
citiz
en s
cien
ce
SUGGESTIONS / OBSERVATIONS
• Continue to build on existing standards Ensure that domain-specific infrastructures are cross-compatible, at a minimum
• Keep it simpleComplexity—even if it’s under wraps—could be at odds with the needs of citizen scientists
• Focus on the user rather than the observerCitizens want to make a difference, so ensure that their data helps users first and foremost
www.gbif.org
Kyle [email protected]
gbif.orgTwitter @gbifFacebook gbifnewsLinkedIn linkedin.com/grp/home?gid=55171Github github.com/gbif
GBIF Ebbe Nielsen Challenge gbif.devpost.com
gbif2.devpost.com
