An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations. e-Infrastructures allow scientists residing at distant places to collaborate. They offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction, e.g. data transfer, data harmonization, data processing workflows etc. e-Infrastructures are gaining an important place in the field of biodiversity conservation. Their computational capabilities help scientists to reuse models, obtain results in shorter time and share these results with other colleagues. They are also used to access several and heterogeneous biodiversity catalogues. In this course, the D4Science e-Infrastructure will be used to conduct experiments in the field of biodiversity conservation. D4Science hosts models and contributions by several international organizations involved in the biodiversity conservation field. The course will give students an overview of the models, the practices and the methods that large international organizations like FAO and UNESCO apply by means of D4Science. At the same time, the course will introduce students to the basic concepts under e-Infrastructures, Virtual Research Environments, data sharing and experiments reproducibility.

1. Using e-Infrastructures for
Biodiversity Conservation
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 researchers in 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
Virtual Research 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 both a 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
Large Set 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

7. Geospatial Data

8. • Geospatial data: description and access
• Catalogues
• Visualisation
• Processing
• Processing examples
• Use Case: the European Geothermal Information
Platform

9. Geospatial data
• Data that 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 feature need 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
• Several solutions 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 systems are 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

15. Mercator projection
Google
Open Layers
Equirectangular projection

16. OGC Standards
Some standards:
Web Maps 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 and Formats:
• 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
• Describe metadata 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 in a 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

22. Online examples:
GeoNetwork
http://geonetwork.d4science.org/geonetwork/
http://geonetwork.geothermaldata.d4science.org/geonetwork/srv/en/
main.home

23. • Geospatial data: description and access
• Catalogues
• Visualisation
• Processing
• Processing examples
• Use Case: the European Geothermal Information
Platform

24. Geo-spatial Data in i-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 Discovery and Visualization
25
Layers Stack
Functions
Visualization
Discovery Metadata

26. Examples and Exercises:
the i-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 Resolution Grid
In Z and T
D4Science Data Resources
D4Science Projector
Modelling Layer
Matrices of data in time
GeoTiff

29. Advantages of Geo Modelling
• 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 in Z 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
• Species Distribution
maps
• Environmental layers
• SAR Images

33. Occurrences Enrichment
Associate Environmental information to a set of occurrence points of a
species
Environmental values grid
Occurrence Points

34. Periodicity and Seasonality
Periodicity: 12 monthsExtraction Tools Fourier Analysis

35. Environmental Signal Processing
Resampling
Spectrogram

36. Water/Height Column
Given a layer 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 potential niche 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 for Geothermal 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

40. Architecture
40
Visualization:
GeoExplorer
Processing:
Statistical
Manager
Documents
Sharing:
Workspace
Social
EGIP
GeoNetwork
GeoServer
Italy
GeoServer
Hungary
GeoServer
Switzerland
MapServer
France
D4S
I.S.
GeoServer
[Others]

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 and aggregate
Information
• Energy Production Trends
per country and year

44. Data Catalogue
44
• The Geonetwork 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 EGIP Web portal
http://egip.d4science.org