a pilot project for biodiversity and climate change interoperability in the geoss framework...

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

[email protected], [email protected]

Biodiversity Information Standards (TDWG)Annual Conference 2007

Bratislava, Slovakia16-22 September 2007


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


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


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.


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


• 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


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


The Demonstration solutionsThe Demonstration solutions


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


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


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


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


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


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


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


6. Put together a demonstrator user interface

• Demo AJAX Graphical User Interface running on your Web Browser


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


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


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


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>>


Demo MovieDemo Movie


Live DemoLive Demo

AJAX GUI URL: http://prometeo.pin.unifi.it/om/GBIFClient.html


Thank you!

Questions?

Back-up Slides


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


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


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


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


Search by classification: Example

•Based on the GBIF data portal classification


Summary:

Open ModelerActivity

Diagram

Apply GARP, BioClimand other models

Ecological Niches

Distributional Shifts

CategoricalClimate Maps

Region Shift

Distributional Shifts inEcological Niches


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


Example: data-provider metadata mapping

metadata:identificationInfo

metadata:distributioninfo


Example: taxon metadata mappingmetadata:identificationInfo


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)


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


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)


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


Three Possible Climate Change scenarios

Source: NCAR/GIS http://www.gisclimatechange.org


Different behaviours


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>>

a pilot project for biodiversity and climate change interoperability in the geoss framework...

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