1 Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Integrating Biodiversity Datasets - the case of GBIF Éamonn Ó Tuama.

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/

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 6

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 7

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 9

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 10

http:/data.gbif.org

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 11

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 12

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 13

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.

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 14

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 15

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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Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 17

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 18

(TDWG GML1 application schema)

Open Geospatial Consortium (OGC) Web Services

Web Map Service

Web Feature Service

Web Coverage Service1Geography Markup Language

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 19

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 21

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 22

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 23

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 24

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

Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 25

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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