GEO task AR-06-01
IP3 Meeting
Vienna, 16 April 2007
GEOSS GBIF Interoperability
Process Pilot Project
S. Nativi1, H. Saarenmaa2, P. Mazzetti1, S. J.
Singh Khalsa3, L. Bigagli1
National Research Council – IMAA and Univ. of Florence
2 GBIF Secretariat
3 National Snow and Ice Data Center - University of Colorado
1 Italian
Outline
• Rationale
– IP3 Phases II and III
• GBIF Interoperability Scenario
• Demo Objectives
• Demo Short-term Steps
– AJAX-SOAP client for OpenModeller
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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
another system
– 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
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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
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GBIF Interoperability Scenario
• Biodiversity and Climate Change
– The theme for the International Day for
Biological Diversity (IBD) in 2007
– will be celebrated on 22 May
• The expectations for a successful demo
are high
– recent global attention on this topic
– report of the Intergovernmental Panel on
Climate Change
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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
– 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 OpenModeller project
– An open framework
– A set of web services
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The GBIF Interoperability approach
Ecological
Niche Modelling
OpenModeller
Server
Biodiversity
Records
GBIF
Registry
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Climatological & Environ.
Data
GEOSS
Registry
Demo Objectives
• Specific
– Study the biodiversity adaptation to climate
change
• General
– Address significant environmental problems
• combining GBIF and other GEOSS data
• using open modelling frameworks
– Demonstrate a methodological study
• an open access framework that uses GBIF data in
wider contexts.
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Short-term demo steps
1. Write a formal and expanded use scenario
– Candidate: Modeling the impact of climate change on the distribution of the
butterflies of Canada and Alaska.
2. Use GBIF web services to access and retrieve Canadian and Alaskan
butterfly data for the pilot
– using GBIF Data Portal centrally
– getting the data from the individual data providers.
3. Access and retrieve via Web Services climatological data for all months
of the year for the past 30 years or more (one degree cells of
resolution)
– average temperature layers
– rainfall layers
– land cover layers
4. Run the Open Modeller Web services using the SOAP interface
– Upload of both Climatological and Biodiversity layers
– Create and run models
– Get outputs
5. Put together a demonstrator user interface, possibly using the GEO
Portal which already has this kind of display features
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OpenModeller
• A flexible, user friendly,
cross platform
environment where the
entire process of
conducting a fundamental
niche modeling experiment
can be carried out.
• Client-server architecture
enabling the existence of
different client interfaces
(desktop, command line
and web-based).
• Tasks can be performed in
a distributed way, including
the possibility of running
separately the algorithms
in remote cluster
machines.
• Source code is available at
sourceforge.
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Open
Modeler
Activity
Diagram
Apply GARP, BioClim
and other models
Ecological
Niches
Distributional Shifts
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Categorical
Climate Maps
Region Shift
Distributional Shifts in
Ecological Niches
Outputs
• Social Benefit
– Historical distribution maps and predicted distributions
under different climate change scenarios for the
selected species
– Graphs summarizing the statistics of range change
for a large number of species.
• Technology
– Outlining of an automated process for producing
these data from GBIF data sources and the GEOSS
interoperability framework.
– Enabling any scientific user to do these analyses
much faster and using much larger datasets than has
been possible before.
nativi@imaa.cnr.it
GBIF Web Server
Registry
Data
GBIF Web Server
Engineering View
Data
Registry
GEOSS Web Server
GEOSS Web Server
Registry Data
Registry
Data
<<artifact>>
Environmental data
<<artifact>>
Distribution Data
<<artifact>>
GCM outputs
<<artifact>>
Distribution Data
Clearinghouse & Mediation Web Server
Data Discovery
Data evaluation
<<artifact>>
Output
GBIF IP3 Workflow Engine (UseCase #)
GUI
execute task
<<artifact>>
Echo Niches
Run GARP model
<<artifact>>
Regional shifts
Run Regional Shift model
Biodiversity Model Web Server
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Data Access
<<artifact>>
Echo niche shifts
Run Distribution Shift model
Back-up slides
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AJAX-SOAP Client for OpenModeller
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AJAX-SOAP Client for OpenModeller
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AJAX-SOAP Client for OpenModeller
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AJAX-SOAP Client for OpenModeller
Time
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AJAX-SOAP Client for OpenModeller
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AJAX-SOAP Client for OpenModeller
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Phase I
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Objectives
•
The main objectives of this Phase are:
1. Describe the present Biodiversity
interoperability framework
– in the context of the more general geospatial
information interoperability framework
– to discover and access other geospatial
resources, and viceversa;
2. Report the main experiences and projects
which have been pursuing this objective
1. try to harmonize them to make the best from the
available resources.
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Actions
•
The main actions of this Phase are:
1. Identify de-jure and de-facto standards, for
•
•
Data & Metadata Models
Service Protocols
2. Identify interoperability agreements in use
3. Analyze successful data integration projects
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Biodiversity standards
• Metadata main models
– ABCD
– Darwin Core
– CBD controlled vocabulary
• Access/discovery protocols
– BioCASE
– DiGIR
– TAPIR (TDWG Access protocol)
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Used ICT standards
• Main modeling and encoding languages used by the
Biodiversity Community
– DCMI
– RDF
– XML
• Main communications approach used by the Biodiversity
Community
– REST-ful approach
• Registry protocol used by the Biodiversity Community
– UDDI
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Useful Projects initiatives
• CBD Clearinghouse
– Signed by 150 government leaders at the 1992 Rio Earth Summit, the
Convention on Biological Diversity is dedicated to promoting sustainable
development. Conceived as a practical tool for translating the principles of
Agenda 21 into reality, the Convention recognizes that biological diversity is
about more than plants, animals and micro organisms and their ecosystems
– it is about people and our need for food security, medicines, fresh air and
water, shelter, and a clean and healthy environment in which to live.
– The Clearing-House is coordinated by the Executive Secretary and overseen
and guided by an Informal Advisory Committee (IAC) set up by the Parties to
the Convention. The committee works in a transparent and cooperative
manner to promote awareness of the multiple needs and concerns facing
various communities, countries and regions.
– In addition, a network of national focal points for the mechanism is being
established to address matters relating to technical and scientific
cooperation. The Parties have recently emphasized the need to strengthen
the role of these focal points. Building a network of non-governmental
organizations and other institutions working on biodiversity could contribute
to this goal. Establishing National, Regional, Subregional and Thematic
Clearing-House Focal Points for specific topics could also help.
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Useful Projects and initiatives
• GBIF
– GBIF is an open-ended international co-ordinating body set up
with the overall aim of furthering technical and scientific efforts to
develop and maintain a global information facility for sharing of
digital biodiversity data
• BioCASE
– The Biological Collection Access Service for Europe, BioCASE,
is a transnational network of biological collections of all kinds.
BioCASE enables widespread unified access to distributed and
heterogeneous European collection and observational
databases using open-source, system-independent software and
open data standards and protocols
• GEO Biodiversity Task BI-06-02
– Building on the framework adopted for monitoring biodiversity
trends in the UN Convention on Biological Diversity, conduct a
series of workshops and meetings to (i) define the needs and
requirements of the biodiversity information users sector, (ii)
delineate available methodologies and (iii) identify the adequacy
of current and past observational strategies
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Useful Projects and initiatives
• GTOS
– GTOS is a programme for observations, modelling, and analysis of
terrestrial ecosystems to support sustainable development.
– GTOS facilitates access to information on terrestrial ecosystems so that
researchers and policy makers can detect and manage global and
regional environmental change.
• TDWG
– The International Working Group on Taxonomic Databases (TDWG) is a
not-for-profit, scientific and educational association formed to establish
international collaboration among the creators, managers and users of
biodiversity information so as to promote the wider and more effective
dissemination of information about the world's heritage of biological
organisms for the benefit of the world at large.
– To achieve its goals, TDWG: a) develops, adopts and promotes
standards and guidelines for the recording and exchange of data about
organisms; b) promotes their use through the most appropriate and
effective means; c) acts as a forum for discussion through meetings and
publication.
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Useful Projects and initiatives
• DIVERSITAS
– DIVERSITAS brings together biological, ecological and social sciences
to address four key questions that underlie our limited understanding of
the current situation.
• How did biodiversity evolve in space and time to reach current state?
• How much biodiversity exists and how does its change or loss affect the
system as a whole?
• How does biodiversity correspond to the delivery of ecosystem functions and
services, and what is the true value of these commodities?
• How can scientific investigation support policy and decision making to
encourage more sustainable use of biodiversity?
– DIVERSITAS activities are guided by the Scientific Committee (SC),
which comprises leading scientists from around the globe.
Representatives from each of the founding Sponsors and Chairs of the
global environmental change programmes that comprise the Earth
System Science Partnership (IHDP, IGBP, and WCRP) serve in an exofficio capacity.
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Useful Projects and initiatives
• speciesLink
– A distributed information system that integrates primary data from biological
collections of the State of São Paulo, Parana's network Taxonline, the SICol
network, Rio de Janeiro Botanical Garden Herbarium and observation data from
the Biota/Fapesp program, and some collections outside of Brazil.
• LTER
– The Long Term Ecological Research (LTER) Network is a collaborative effort
involving more than 1800 scientists and students investigating ecological
processes over long temporal and broad spatial scales. The Network promotes
synthesis and comparative research across sites and ecosystems and among
other related national and international research programs. The US National
Science Foundation established the LTER program in 1980 to support research
on long-term ecological phenomena in the United States. The 26 LTER Sites
represent diverse ecosystems and research emphases. The LTER Network
Office coordinates communication, network publications, and research-planning
activities.
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Useful Projects and initiatives
•
ALTER-Net
– ALTER-Net is a five year project funded by the European Union's Framework VI
programme. ALTER-Net is a Network of Excellence: its 24 partner institutes from
17 European countries are aiming to build lasting integration of biodiversity
research, monitoring and communication capacity. ALTER-Net is integrating
capacity across Europe to assess and forecast changes in biodiversity, structure,
functions and dynamics of ecosystems and their services. This is being achieved
in a number of ways. ALTER-Net is a focus of efforts to create a network of sites
for European long-term terrestrial and freshwater biodiversity and ecosystem
research (Long-Term Ecosystem Research sites, LTER). It is also developing a
related network of Long-Term Socio-Ecological Research (LTSER) sites, which
could be used to determine the socio-economic implications of, and public
attitudes to, biodiversity loss.
•
LTER
– The Long Term Ecological Research (LTER) Network is a collaborative effort
involving more than 1800 scientists and students investigating ecological
processes over long temporal and broad spatial scales. The Network promotes
synthesis and comparative research across sites and ecosystems and among
other related national and international research programs. The US National
Science Foundation established the LTER program in 1980 to support research
on long-term ecological phenomena in the United States. The 26 LTER Sites
represent diverse ecosystems and research emphases. The LTER Network
Office coordinates communication, network publications, and research-planning
activities.
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Useful Projects and initiatives
• United Nations Environment Programme World Conservation
Monitoring Centre
– To evaluate and highlight the many values of biodiversity and put authoritative
biodiversity knowledge at the centre of decision-making. To be an internationally
recognized Centre of Excellence for the synthesis, analysis and dissemination of
global biodiversity knowledge, providing authoritative, strategic and timely
information for conventions, countries, organizations and companies to use in the
development and implementation of their policies and decisions. The Centre has
a mandate from the UNEP Governing Council to provide a range of biodiversityrelated services to UNEP, the biodiversity-related conventions and their
constituent party-states and other bodies in the non-governmental and private
sectors.
• Open Geospatial Consortium (OGC) and TDWG memorandum of
understanding
– to develop profiles and schemas of OGC standards based on the TDWG's
international framework for representation of biological organisms. The TDWG
and the OGC will collaborate in the development of profiles and schemas of
OGC standards such as the Geography Markup Language (GML) and TDWG
standards for representation of location of biological specimens, organisms and
their distributions, communities, movements, etc. Joint activities may involve
testbeds and interoperability experiments on the spatial representation of
biodiversity. The two groups will also collaborate on outreach.
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Successful projects and initiatives
already contacted
• Possible collaborations and/or concerted actions
are under discussion with:
– Task BI-06-02 of GEOSS, led by DIVERSITAS, in partnership
with GBIF and GTOS, and the GEOSS secretariat
• Contact persons: N Jürgens and A Larigauderie
– GBIF Secretariat and Community
• Contact person: Hannu Saarenmaa
– Task group inside TDWG called SubStandards or BioGeoSDI
• Contact person: Javier de la Torre
– OGC for biodiversity outreach
• Contact person: George Percivall
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