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A Pilot Project for Biodiversity and Climate Change Interoperability in
the GEOSS Framework
S.Nativi, P.Mazzetti, L.Bigagli, V.Angelini, E.Boldrini,
É. Ó Tuama, H.Saarenmaa, J.Kerr, S.J.S.Khalsa
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Biodiversity Information Standards (TDWG)Annual Conference 2007
Bratislava, Slovakia16-22 September 2007
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
GBIF IP3 Working Group• GBIF Secretariat
– Éamonn O Tuama, Tim Robertson, Dave Martin, Donald Hobern
• IEEE & University of Colorado– Siri Jodha Khalsa
• Italian National Research Council (CNR-IMAA) & Univ. of Florence– Stefano Nativi, Paolo Mazzetti, Lorenzo Bigagli, Enrico
Boldrini, Valerio Angelini, Ugo Mattia
• University of Ottawa– Jeremy Kerr
• University of Helsinki– Hannu Saarenmaa
• University of Tokyo– Motomi Ito
• WMO– David Thomas
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Outline• Interoperability scenarios between
Biodiversity and Climate Change
• Adopted Solutions for the demonstrations– Datasets and their servers– Federated catalog– Information, computational and engineering
views
• Demonstration
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
GEOSS IP3 (Interoperability Process Pilot Projects)
• Main Objectives– Begin implementing GEOSS Clearinghouse and testing the
processes – Lead up to a suite of demonstrations at a GEO Plenary– Implement a service register for different SBA
• Biodiversity is one of these
• GBIF Interoperability Scenario– Scenarios for interoperability between Biodiversity and Climate
Change SBAs.
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
GBIF Interoperability Scenario• A technique called Ecological Niche Modelling (ENM)
– The scientific approach for using primary biodiversity data for studying adaptation to various climate change scenarios has been created by Peterson & al. (2001, 2002).
• GBIF has been promoting this approach– GBIF has integrated 118 million primary biodiversity records from
about 1000 databases, – GBIF has opened prototype web services to access them through
a one stop shop
• The modelling tools for ENM are being made available through the Open Modeller project– An open framework– A set of web services
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
• Biodiversity Data– availability of data– biological and ecological representativeness– expected susceptibility– Importance– on-line accessibility
• Climate Change Data– to find/generate useful parameters
• e.g. temperature, rainfall, vegetation, land use cover, etc– to span at least 30 years– to cover the useful areas
• georeferentiation• right resolution (e.g. 0.25x0.25 degree)
– on-line accessibility
Demonstration: requirements & issues
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Demonstration: requirements & issues
• Ecological Niche Modelling (ENM)– On-line accessible functionalities
• E.g. Web services
– To support different type of models
• Interoperability– Federated catalog to discover, query and evaluate
heterogeneous resources in a distributed way
• User Accessibility – To provide users with a neutral and simple client
application• e.g. AJAX application on a Web Browser
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
The Demonstration solutionsThe Demonstration solutions
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Adopted solutions1. Write a formal and expanded use scenario
2. Use GBIF portal web services to access and retrieve the biodiversity data
3. Access and retrieve NCAR Climate Change data via OGC WCS
4. Interoperability with GBIF and Climate registries using GI-go/GI-cat federated catalog and Mediation Server (ISO19115 core metadata)
5. Use the Open Modeller ENM framework through its SOAP functionalities
6. Put together an AJAX based demonstrator user interface
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
1. Write a formal and expanded use scenario
• Modeling the impact of climate change on the distribution of the butterflies of Canada and Alaska– Scientific name = amblyscirtes vialis – Species taxonomy:
• Animalia->arthropoda
->insecta->lepidoptera
->hesperiidae->amblyscirtes
->amblyscirtes vialis
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
2. Use GBIF web services to access and retrieve the biodiversity data
• International organisation launched under the OECD Megascience Forum in 2001– 40 countries, 33 int’l organisations members
• Network of primary data– 200 providers in 30 countries, connecting over 1000 databases,
124 million records of in-situ observations• Building on Biodiversity Informatics Standards
(www.tdwg.org)– Darwin Core, ABCD, DiGIR, BioCASE, TAPIR, ...– MoU with OGC
• Infrastructure– UDDI Registry, Data Portal, Cache of all data, Web Services
• GBIF Central Data Portal – supports data validation and cleaning tasks
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
3. Access and retrieve via OGC WCS Climate Change data
• Data Source– GIS Climate Change Scenarios project conducted by the
NCAR GIS Initiative– Provide Web access to free global datasets of climate
change scenarios• generated for the 4th Assessment Report of the
Intergovernmental Panel on Climate Change (IPCC) by the Community Climate System Model (CCSM). http://www.gisclimatechange.org
• Served through a WCS server– Downloaded from the NCAR GIS portal– Processed to generate Grid Coverages– Uploaded data and metadata to a WCS 1.0 server
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
3. Access and retrieve via OGC WCS Climate Change data
• Climate model outputs considered– Time
• Present situation in: 2000• Future situations in: 2010, 2020, 2030, 2040, 2050 for 3 different
climate change scenarios (named A1, B1, A1B)• 1 month of resolution
– Space• 1 x 1 degree of resolution
– Parameters TS Surface Temperature
PRW Atmosphere Water Vapor Content
PR Precipitation Flux
PRSN Snow Fall Flux
CLWVI Atmosphere Cloud Condensed Water Content
MRRO Runoff Flux
MRSO Soil Moisture Content
Minimum and maximum monthly average surface temperatures are generatedMinimum and maximum monthly average surface temperatures are generated
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
4. Interoperability with GBIF and climatological registries
• Mediation Metadata Model: ISO 19115 core profile
WCSRegistry
Climatological and Environmental Data
Processing onDistributed
OpenModellerComputeServers
In-situBiodiversityRecords
GBIF Registry
GI-cat/GI-go
Discovery DownloadDownload
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
5. Run ENM using the OpenModeller Framework
• Run the Open Modeller Web services using the SOAP interface
• Upload of both Climate Change and Biodiversity layers
– Discovered through GI-cat
• Create and run models
• Get model output maps
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
6. Put together a demonstrator user interface
• Demo AJAX Graphical User Interface running on your Web Browser
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Information View
• Geospatial/GBIF interoperability
• Data model Mediation
– GBIF to ISO 19115 concepts
– GBIF to ISO 19115 Core metadata elements
• Functional Adaptation– Resource discovery
– Resource querying
– Resource access• Preview
• Download
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Mapping of GBIF concepts to ISO hierarchical data model
Data provider
GBIF data model concepts GBIF data model concepts ISO data model concepts ISO data model concepts
GBIF new portal Catalog
Dataset collection
Data resource Dataset
Taxonomy element Metadata
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
GBIF Server
ENMServer
Climate Change Server
Q uerygetM etadata
Q uerygetM etadata
D ownload D ownload
Computational View
Q uerygetM etadata
Federated Catalog &Mediation Server
Discovery/Access
getC ontentgetM etadataquery
1
Messaging
publishsubscribeunsubscribe
Session
com m itin itlogin
Distribution
addrem ove
Repository
purgestore
Mediation
getM appingsetM apping
logoutrollback
0..1 0..1 0..1 0..1 0..1
GBIF - MediationOGC W CS - Mediation
Use ScenarioController
U ploadR un
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
GBIF Server
ENMServer
Climate Change Server
Q uerygetM etadata
Q uerygetM etadata
D ownload D ownload
Computational View
Q uerygetM etadata
Federated Catalog &Mediation Server
Discovery/Access
getC ontentgetM etadataquery
1
Messaging
publishsubscribeunsubscribe
Session
com m itin itlogin
Distribution
addrem ove
Repository
purgestore
Mediation
getM appingsetM apping
logoutrollback
0..1 0..1 0..1 0..1 0..1
GBIF - MediationOGC W CS - Mediation
Use ScenarioController
U ploadR un
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Data Proxy<<Web Application Server>>Data Store
OpenModeller Server<<Biodiversity Model Web Server>>
Run GARP model Run Regional Shift model Run Distribution Shift model
GI-Go/GI-Cat<<Federated Catalog & Mediation Server>>
Data Discovery Data AccessData evaluation
Climate Data Server<<WCS server>>
describeCoverage getCapabilities
GUI<<AJAX component>>
GBIF Portal Server<<Web Server>>
Occurrence Taxon
download
File System<<Data Stotage>>
uploaddownload
getCoverage
Eng
inee
ring
Vie
w Taxonomy Data<<artifact>>
Occurrences data<<artifact>> Climate Forecasts
<<artifact>>
Environmental data<<artifact>>
Output<<artifact>>
Echo Niches<<artifact>>
Regional shifts<<artifact>>
Echo niche shifts<<artifact>>
Data Representation<<artifact>>
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Demo MovieDemo Movie
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Live DemoLive Demo
AJAX GUI URL: http://prometeo.pin.unifi.it/om/GBIFClient.html
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Thank you!
Questions?
Back-up Slides
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Discovery Functionality Mapping
•GI-cat Discovery Functionality
getContent(portal)
getContent(provider)
getContent(resource)
getContent(taxon)
GBIF taxon service/list & get action
–for each provider p of interest:taxon/list?dataproviderkey=p.key&rank=kingdom(Also provides information on data resources)
taxon/get/taxon.key
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Phase 2 – Cross-System Interoperability Scenarios
• Develop scenarios that require the exchange of data and information between GBIF and other disparate systems– Address needs identified in one or more of the Societal Benefit
Areas.– Ensure relevancy
• Create interoperability arrangements between GBIF and other systems – Analyze the entries in the GEOSS Service Register for the
systems to be made interoperable. Where the registered standards are insufficient to support interoperability, work with technical experts to identify solutions
– When a solution is identified it will be circulated for approval and, upon acceptance, this arrangement will be entered into the Interoperability Register
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Phase 3 – Demonstrations
• Share Phase 2 results first with the Architecture and Data Committee and then with all GEO Members and Contributing Organizations – Present a briefing on the process – Give a live demonstration of those infrastructure
components that have been implemented at that time • The Interoperability Register and Registry• Data and information exchange via the defined arrangements
• Two kinds of demonstrations– technical demo;– social benefit demo for policy makers and Senior
Managers, to illustrate interoperability process and its benefits
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Ortalis poliocephala
in Mexicobefore (green)
vs. after (red)
Biodiversity & Climate Change & Land Use scenario
Town Peterson & al. 2002
The species will be pushed
to marginal areas
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Search by classification: Example
•Based on the GBIF data portal classification
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Summary:
Open ModelerActivity
Diagram
Apply GARP, BioClimand other models
Ecological Niches
Distributional Shifts
CategoricalClimate Maps
Region Shift
Distributional Shifts inEcological Niches
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Lesson learned and Future work
• Component Services– Documentation must be improved– More testing is needed – Improve flexibility and configurability
• Interoperability– Need for special interoperability arrangement among
communities– Improve interface and protocol standardization– Improve dataset encoding standardization– Stress SOA driven approaches
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Example: data-provider metadata mapping
metadata:identificationInfo
metadata:distributioninfo
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Example: taxon metadata mappingmetadata:identificationInfo
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Functional Mapping
•GI-cat Discovery Function
GBIF taxon service
GI-cat Query Function
Query criteria
Area
Time
Free text
Hierarchy
GBIF occurrence service
List parameters
minlatitude, maxlatitude, minlongitude, maxlongitude
startdate, enddate
scientificname
dataproviderkey, dataresourcekey
(Where, When, What, Who)
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Functional Mapping
GI-cat Access Function
Download
Preview
GBIF occurrence service
Stripping of occurrence overview (from GBIF portal)
Example: bounding box over
canada scientific name is
“amblyscirtes vialis” Resource is University of
Alberta Museums
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Text search
•GI-cat text search
–Free text search
• search engine-like syntax
GBIF supports two types of text search:free text search on
scientific nameonly OR operation is
supportedresults are exact matches
or initial exact matches
Controlled dictionary search on taxonomy
search includes synonims and subconcepts
Search by classification(introduced)
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Federated Catalog &Mediation Server
Discovery/Access
getC ontentgetM etadataquery
1
Messaging
publishsubscribeunsubscribe
Session
com m itin itlogin
Distribution
addrem ove
Repository
purgestore
Mediation
getM appingsetM apping
logoutrollback
0..1 0..1 0..1 0..1 0..1
GBIF Server
ENMServer
Use ScenarioController
GBIF - MediationOGC W CS - Mediation
Climate Change Server
U ploadR un
Q uerygetM etadata
Q uerygetM etadata
Q uerygetM etadata
D ownload D ownload
Computational View
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Three Possible Climate Change scenarios
Source: NCAR/GIS http://www.gisclimatechange.org
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Different behaviours
nativi@imaa.cnr.it, boldrini@imaa.cnr.it
Data Proxy<<Web Application Server>>Data Store
OpenModeller Server<<Biodiversity Model Web Server>>
Run GARP model Run Regional Shift model Run Distribution Shift model
GI-Go/GI-Cat<<Federated Catalog & Mediation Server>>
Data Discovery Data AccessData evaluation
Climate Data Server<<WCS server>>
describeCoverage getCapabilities
GUI<<AJAX component>>
GBIF Portal Server<<Web Server>>
Occurrence Taxon
download
File System<<Data Stotage>>
uploaddownload
getCoverage
Eng
inee
ring
Vie
w Taxonomy Data<<artifact>>
Occurrences data<<artifact>> Climate Forecasts
<<artifact>>
Environmental data<<artifact>>
Output<<artifact>>
Echo Niches<<artifact>>
Regional shifts<<artifact>>
Echo niche shifts<<artifact>>
Data Representation<<artifact>>
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