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Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 1
Integrating Biodiversity Datasets
- the case of GBIF
Éamonn Ó Tuama
GBIF Secretariat,
Universitetsparken 15
DK-2100 Copenhagen Ø
Denmark
email: [email protected]
Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 2
Outline
Role of GBIF in biodiversity informatics
GBIF web services & geospatial web
The GBIF architecture
Using GBIF mediated data -
Assessment of Climate Change Impact
Indicators of Compliance with 2010 Target
Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 3
GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ØGBIF has five main programmes of work
Outreach and capacity building (OCB)
4 Themes
Informatics
Content
Participation
Campaigns
Digitisation of natural history collections (DIGIT)
Building regional and local infrastructure (NODES)
Electronic catalogue of names of known organisms (ECAT)
Data access and database interoperability (DADI)
Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 4
Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 5
http://www.tdwg.org/
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Core data types on GBIF network
Taxon names Taxon occurrence information
specimen records from natural history collections
observational records
Fields used in indexing records
Mandatory Scientific name Institutional code Collection code Catalogue number
Highly desirable Geospatial location Collection date Higher taxon info Date last modified
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Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 8
datasets metadata
name providers
datasets metadata
data providers
registry
institutionsprovidersservices
index
metadata data cache
logging
data portal
queryengine
request handling web services
Components of GBIF Architecture
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Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 10
http:/data.gbif.org
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Web Services
Software applications that run over the internet and use some kind of standardised message passing system to handle request and response, usually based on XML.
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GBIFData Portal
Web Services
occurrence record datahttp://data.gbif.org/ws/rest/occurrence
occurrence density datahttp://data.gbif.org/ws/rest/density
dataset metadatahttp://data.gbif.org/ws/rest/resource
data provider metadatahttp://data.gbif.org/ws/rest/provider
data network metadatahttp://data.gbif.org/ws/rest/network
http://data.gbif.org/ws/rest/taxon taxon data
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GBIF Occurrence Web Service
http://data.gbif.org/ws/rest/occurrence/<action>?<parameter_list>
Main actions: Get, List, Count
Parameter list: key-value pairs
http://data.gbif.org/ws/rest/occurrence/list?
scientificname=Ensis+ensis&format=darwin-1.2
http://data.gbif.org/ws/rest/occurrence/get/801914
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GBIF Occurrence Web Service
scientificname
taxonconceptkey
dataproviderkey
datasourcekey
resourcenetworkkey
basisofrecord
minlatitude
maxlatitude
minlongitude
maxlongitude
cellid
georeferencedonly
hostisocountrycode
originisocountrycode
startdate
enddate
modifiedsince
startindex
maxresults
format
icon
mode
stylesheet
Parameter list: keys
http://data.gbif.org/ws/rest/occurrence
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(TDWG GML1 application schema)
Open Geospatial Consortium (OGC) Web Services
Web Map Service
Web Feature Service
Web Coverage Service1Geography Markup Language
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integrating national and thematic portals
Coastlines,Marine areas,Remote sensing imagery
Occurrences,Names
Meteorological,Oceanographic
data data data
Web MapService
Web FeatureService
Web CoverageService
The Geospatial Web
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Ecological Niche Modelling a modelling technique for defining the ecological
requirements of a species – its ecological niche
many different algorithms in use (e.g. Maxent, GARP)
an algorithm uses a set of environmental variables (e.g. topographic, climatic) to define the ecological niche
once the ecological niche is defined it can then be used to query a set of environmental conditions (e.g. as predicted by a climate change model) to determine the potential distribution of the species
outputs as maps, statisticsSource: http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf
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GBIF mediated data can, in principle, be used, in pursuit of CBD 2010 objectives -
to provide indices of “trends in the abundance and distribution of selected species”
to develop indices of any kind of “selected species”
to develop indices at national, regional or global levels
Source: http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf
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GBIF mediated data can be used to develop temporally-organised indicators to measure the effects of land-use change on the distribution of species
Change in distributional area of species over time
Source: http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf
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Using GBIF mediated data can be used to measure the impact of climate change on species distributions
Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007”
Source:
Working within the GEOSS / GMES framework
Climate Change
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a) distribution derived from historical observations of climate, land use, and species location from 1900-1930
Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007”
Source:
Climate Change
Distribution of Vanessa atalanta
ba
b) distribution derived from models run on the same data from 1960-1990
The species has expanded its range over time
Species can be highly responsive to climate change
Vanessa atalanta; Photo by Jeremy T.Kerr – August 1, 2005. Ottawa, Ontario
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Acknowledgements
The modelling scenarios in this presentation are based on publications by Peterson & Soberón1 and Nativi et al.2
Thank you
data.gbif.orgPredicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007”
Development of indicators of compliance with the 2010 target of the convention on biological diversity using primary biodiversity data provided by GBIF. A.T.Peterson & J. Soberón. http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf
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