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Uploaded byGianpaolo Coro
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 2
The document discusses the use of e-infrastructures for biodiversity conservation, focusing on tools, platforms, and data management solutions that facilitate international collaboration among researchers. It emphasizes geospatial data handling, including methods for visualization, processing, and the importance of standards set by the Open Geospatial Consortium. A specific case study is presented on the European Geothermal Information Platform (EGIP) which aims to provide accessible geothermal data to stakeholders.
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USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 2
- 1. Using e-Infrastructures for BiodiversityConservation Gianpaolo Coro ISTI-CNR, Pisa, Italy
- 2. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform Module 2 - Outline
- 3. e-Infrastructures “e-Infrastructures enable researchersin different locations across the world to collaborate in the context of their home institutions or in national or multinational scientific initiatives. They can work together by having shared access to unique or distributed scientific facilities (including data, instruments, computing and communications)*.” Examples: *Belief, http://www.beliefproject.org/ OpenAire, http://www.openaire.eu/ i-Marine, http://www.i-marine.eu/ EU-Brazil OpenBio, http://www.eubrazilopenbio.eu/
- 4. Virtual Research Environments VirtualResearch Environments: virtual organizations of communities of researchers for helping them collaborating. • Define sub-communities inside an e-Infrastructure; • Allow temporary dedicated assignment of computational, storage, and data resources to a group of people; • Very important in fields where research is carried out in several teams which span institutions and countries. e-InfrastructureVRE VRE VRE
- 5. D4Science D4Science is botha Data and a Computational e-Infrastructure • Used by several Projects: i-Marine, EUBrazil OpenBio, ENVRI; • Implements the notion of e-Infrastructure as-a-Service: it offers on demand access to data management services and computational facilities; • Hosts several VREs for Fisheries Managers, Biologists, Statisticians…and Students.
- 6. D4Science - Resources LargeSet of Biodiversity and Taxonomic Datasets connected A Network to distribute and access to Geospatial Data Distributed Storage System to store datasets and documents A Social Network to share opinions and useful news Algorithms for Biology- related experiments
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- 8. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 9. Geospatial data • Datathat identify the geographic location of features and boundaries on Earth • Usually stored as coordinates and topology • Accessed and processed through Geographic Information Systems (GIS)
- 10. Projections • Spatial featureneed to be referenced to a location: – to permit flexible georeferenced visualization – to permit correct measurements – to permit operations between datasets based on different reference systems • Spatial reference systems allow defining positions on the Earth‘s surface • Issue: the Earth is irregular and has spherical shape
- 11. Coordinates Systems • Severalsolutions are possible as coordinates systems: – Cartesian: coordinate values locate a point in relation to mutually perpendicular axes – Polar: coordinates locate a point by angular direction(s) and distance from center. – Spherical: point on surface located by angular measurements from center (latitude, longitude)
- 12. Earth representation • Sphere –simple, for small scale work • Ellipsoid – improved adjustment to ‚real‘ shape • Geoid – not a geometrically, but physically (gravity) defined body. Taken from http://www.geo.info.hu/uniphorm/chapter4_SpRef/up_spatialref/up_spatialref.PPT
- 13. • Coordinate systemsare defined by – number of dimensions (1, 2 or 3) – sequence/name of coordinate values (x, y, z) – unit scaling factor and system (meters) – origin of axes – direction of axes • Coordinate systems can be based on a geodetic reference (datum) and a map projection Coordinate systems
- 14. Geodetic system (geodetic datum):a coordinate system, and a set of reference points, used to locate places on the Earth. E.g.: the World Geodetic System (WGS), a standard for use in cartography, geodesy, and navigation. Comprises a standard coordinate system for the Earth, a standard spheroidal reference surface (reference ellipsoid) for raw altitude data, and a gravitational equipotential surface (the geoid) that defines the nominal sea level. Instance: WGS 84/EPSG:4326 Map projection: a systematic transformation of the latitudes and longitudes of locations on the surface of a sphere or an ellipsoid into locations on a plane E.g.: Equirectangular projection or Mercator projection Example: http://openlayers.org/ol3- cesium/examples/epsg-4326.html
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- 16. OGC Standards Some standards: WebMaps Service (WMS): XML-based protocol that allows to display the datasets on an interactive map viewer; Web Coverage Service (WCS): XML-based representation of space-time varying phenomena (especially used for raster maps) Web Features Service (WFS): XML-based representation for discrete geospatial features (especially used for polygonal maps) The Open Geospatial Consortium (OGC) is an international organization involving more than 400 organizations. Promotes the development and implementation of standards to describe geospatial data content and processing.
- 17. Managed Standards andFormats: • Web Maps Service (WMS) • Web Coverage Service (WCS) • Web Features Service (WFS) • OPeNDAP (Access to NetCDF GRID files) • ESRI GRID raster files (ASC) • GeoTiff D4Science - Supported OGC Standards
- 18. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 19. Data Catalogues • Describemetadata for a geospatial dataset in a structured and standardized way • Indispensable for – all kinds of data transfers – interoperability • Include ISO / CEN / OGC work
- 20. Data Catalogues Usage •Changing from one projection to another • Transformations: – from geographical coordinates to projection – from a source projection, via geographical coordinates, towards target projection – vector data projection – raster data projection
- 21. Data Catalogue ina e-Infrastructure 21 • The Geonetwork web application is accessible through the portal • Users can inspect metadata • Metadata are possibly compliant with the INSPIRE directives* * http://inspire.ec.europa.eu/index.cfm/pageid/62
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- 23. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 24. Geo-spatial Data ini-Marine GeoExplorer is a web application (Portlet) for geo-spatial layers to: • Discover • Inspect • Overlay • Save WMS, WCS, WFS The map depicts the native range (~actual distribution) of Latimeria chalumnae
- 25. GeoExplorer: Data Discoveryand Visualization 25 Layers Stack Functions Visualization Discovery Metadata
- 26. Examples and Exercises: thei-Marine GeoExplorer https://i-marine.d4science.org/group/biodiversitylab/geo-visualisation
- 27. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 28. Geospatial Modelling NetCDF ASC WFS WCS XYZT Table Species Modelling Neural Networks Forecasting Signal Processing Maps Comparison User Defines XY ResolutionGrid In Z and T D4Science Data Resources D4Science Projector Modelling Layer Matrices of data in time GeoTiff
- 29. Advantages of GeoModelling • Accounts for many data formats • The user defines the grid resolution and then data are adapted • Accounts for gaps in the data • The analysis is independent on the format; only works on sequences of matrices • Allows to apply general purpose data mining algorithms to geospatial data
- 30. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 31. Area Selection inZ and Time Select a Bounding Box at fixed Z and Time Produce a table containing environmental values in the selected area ENVRI Workshop, 10-13 Feb. 2014
- 32. Maps Comparison Calculate Similarity • SpeciesDistribution maps • Environmental layers • SAR Images
- 33. Occurrences Enrichment Associate Environmentalinformation to a set of occurrence points of a species Environmental values grid Occurrence Points
- 34. Periodicity and Seasonality Periodicity:12 monthsExtraction Tools Fourier Analysis
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- 36. Water/Height Column Given alayer containing 3D environmental information • Extract the environmental information along Z given X,Y,T at resolution R • Produce charts and ranges
- 37. MaxEnt Produces the potentialniche of a species from env. layers and species observation records Environmental layers Occurrence records Estimated species habitat distribution SM
- 38. • Geospatial data:description and access • Catalogues • Visualisation • Processing • Processing examples • Use Case: the European Geothermal Information Platform
- 39. An Infrastructure forGeothermal data: the EGIP case • European Geothermal Information Platform (EGIP): makes disperse and heterogeneous data available to stakeholder communities in the Geothermal domain • A Pilot e-Infrastructure instance has been created: egip.d4science.org 39
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- 41. Portal and Sharing:egip.d4science.org 41 • The workspace is used to broadcast documents • Documents have metadata described according to the INSPIRE directives
- 42. 42 Visualisation D4Science GeoExplorer for EGIP: •Visualize the Temperature and Heat Flow maps of the contributors • Inspect contents • Get a summary of the metadata
- 43. 43 Processing EGIP GeoNetwork Processing: Statistical Manager • Collect andaggregate Information • Energy Production Trends per country and year
- 44. Data Catalogue 44 • TheGeonetwork Web application is accessible through the portal • Users can inspect metadata • Metadata are 100% compliant with the INSPIRE directives* *http://inspire.ec.europa.eu/index.cfm/pageid/6 2
- 45. Online example: The EGIPWeb portal http://egip.d4science.org