geoss gbif interoperability process pilot project geo task ar-06-01 s. nativi 1, h. saarenmaa 2, p....
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GEOSS GBIF Interoperability Process Pilot Project
GEO task AR-06-01
S. Nativi1, H. Saarenmaa2, P. Mazzetti1, S. J. Singh Khalsa3, L. Bigagli1
1 Italian National Research Council – IMAA and Univ. of Florence2 GBIF Secretariat
3 National Snow and Ice Data Center - University of Colorado
IP3 MeetingVienna, 16 April 2007
Outline• Rationale
– IP3 Phases II and III
• GBIF Interoperability Scenario
• Demo Objectives
• Demo Short-term Steps– AJAX-SOAP client for OpenModeller
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
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
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
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
The GBIF Interoperability approach
Ecological Niche Modelling
GEOSSRegistry
Climatological & Environ.Data
OpenModellerServer
BiodiversityRecords
GBIF 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.
Short-term demo steps1. 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
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.
Open ModelerActivity
Diagram
Apply GARP, BioClimand other models
Ecological Niches
Distributional Shifts
CategoricalClimate Maps
Region Shift
Distributional Shifts inEcological 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.
GBIF Web Server
Registry Data
GBIF IP3 Workflow Engine (UseCase #)
execute task
Biodiversity Model Web Server
Run GARP model Run Regional Shift modelRun Distribution Shift model
GEOSS Web Server
Registry Data
Environmental data<<artifact>>
Clearinghouse & Mediation Web Server
Data Discovery Data AccessData evaluation
Echo Niches<<artifact>>
Distribution Data<<artifact>>
Echo niche shifts<<artifact>>
GBIF Web Server
RegistryData
Distribution Data<<artifact>>
GEOSS Web Server
Registry Data
GCM outputs<<artifact>>
Regional shifts<<artifact>>
GUI
Output<<artifact>>
Eng
inee
ring
Vie
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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 objective1. try to harmonize them to make the best from the
available resources.
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
Biodiversity standards
• Metadata main models– ABCD– Darwin Core– CBD controlled vocabulary
• Access/discovery protocols– BioCASE– DiGIR– TAPIR (TDWG Access protocol)
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
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.
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
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.
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 ex-officio capacity.
• 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.
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.
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 biodiversity-related 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.
Useful Projects and initiatives
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