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. 1. Overview of approaches to biodiversity data
management and analysis
2. Explain how to support a specific community of
practice using a general purpose system
3. Show collection of approaches/models/interfaces
that are applicable also to other domains
Aims of the course

3. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access
Module 1 - Outline

4. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

5. 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/

6. e-Infrastructures
• Data e-Infrastructure: an e-Infrastructure promoting data sharing and consumption.
Addresses the needs of the research activity performed by a certain community.
• Computational e-Infrastructure: an e-Infrastructures offering computational
resources distributed in a network environment. Uses Cloud computing to execute
calculations with a large number of connected computers. Offers collaboration
facilities for scientists to share experimental results.

7. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

8. 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

9. 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.

10. A continuously updated list of events / news produced by users
and applications
User-shared
News
Application-
shared News
Share News
D4Science Social

11. A folder-based file system allowing to manage complex
information objects in a seamless way
Information objects can be
• files, dataset, workflows,
experiments, etc.
• organized
into folders and shared
• disseminated via URIs
• accessed via WebDAV
D4Science Workspace

12. 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

13. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

14. i-Marine
i-Marine is an European funded project.
It aims at establishing and operating a Data and Computational e-Infrastructure supporting the
principles of the Ecosystem Approach to Fisheries Management and Conservation of Marine
Living Resources.
Biodiversity
build and
analyse
species
distribution
and
biodiversity
maps
Geospatial
store,
discover,
access, and
process of
geospatial
data
Statistical
exchange
and process
of statistical
data
Semantic
discover and
bridge
across
knowledge
providers
Physical and
chemical
features
Inventories of
biological
information
Habitat types
Socio-
economic
aspects
Marine
resource
assessment
Fishery
operation,
processingand
trade
Marine
Planning

15. 15
i-Marine Community

16. Online examples:
the i-Marine
Web Portal and basic functions
http://portal.i-marine.d4science.org/

17. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

18. An authoritative use case
Coelacanth (Latimeria chalumnae,
Smith 1939)
Coelacanths were thought to have gone extinct in the Late
Cretaceous, but were rediscovered in 1938 off the coast of
South Africa.
Its current form is closely related to its form 400 million
years ago. It is related to lungfishes and tetrapods.

19. Biodiversity Data
Taxonomies
In biology, a taxon (plural taxa) is a group of one or more populations of an organism
or organisms seen by taxonomists to form a unit.
Introduced by Linnaeus's system in Systema Naturae (10th edition, 1758).
• A taxon is usually known by a particular name and given a particular ranking,
especially if (and when) it is accepted or becomes established
• An accepted taxon is given a formal scientific name, according to nomenclature
codes, e.g. Gadus morhua (Linnaeus, 1758)*
• A "good" or "useful" taxon is one that reflects evolutionary relationships.
* More on scientific names here: http://wiki.i-marine.eu/index.php/Taxa_Merging_Discussion

20. Taxa Representations
Biology
Computer science

21. Biodiversity Data
Occurrence data
Specimen, Human Observations (direct/indirect)
Records of species presence, usually provided by scientific surveys

22. Biodiversity Data Providers
i-Marine hosts biodiversity datasets coming from several data providers:
• Some are remotely accessed and are maintained by the respective owners;
• Other ones are resident in the e-Infrastructure.
Currently, the accessible datasets are:
• Catalogue of Life (CoL)
• Global Biodiversity Information Facility (GBIF),
• Integrated Taxonomic Information System (ITIS),
• Interim Register of Marine and Nonmarine Genera (IRMNG),
• Ocean Biogeographic Information System (OBIS),
• World Register of Marine Species (WoRMS)
• World Register of Deep-Sea Species ( WoRDSS )
Some data providers are collectors of other data providers, but the alignment is not
guaranteed!
The datasets allow to retrieve:
• Occurrence points (presence points or specimen)
• Taxa names

23. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

24. Biodiversity Data Providers
Remote

25. Biodiversity Data Representation
Darwin core:
• An extension of Dublin Core
• Used in Biodiversity Informatics
• Its terms are part of vocabularies and technical specifications developed and
maintained by the Taxonomic Databases Working Group (TDWG)
• Based on taxa, refer to species occurrence in nature as documented by
observations, specimens, samples, and related information
• The Simple Darwin Core is a commonly used specification to share data about
taxa and their occurrences in a simply structured way

26. <?xml version="1.0" encoding="UTF-8"?>
<SimpleDarwinRecordSet xmlns="http://rs.tdwg.org/dwc/xsd/simpledarwincore/"
xmlns:dc="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/terms/"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://rs.tdwg.org/dwc/xsd/simpledarwincore/ http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd">
<SimpleDarwinRecord>
<dc:modified>2006-05-04T18:13:51.0Z</dc:modified>
<dc:language>en</dc:language>
<dwc:basisOfRecord>Taxon</dwc:basisOfRecord>
<dwc:scientificNameID>http://research.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=53548
</dwc:scientificNameID>
<dwc:acceptedNameUsageID>http://research.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=22010
</dwc:acceptedNameUsageID>
<dwc:originalNameUsageID>http://research.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=53548
</dwc:originalNameUsageID>
<dwc:nameAccordingToID>http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=22764
</dwc:nameAccordingToID>
<dwc:namePublishedInID>http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=671
</dwc:namePublishedInID>
<dwc:scientificName>Centropyge flavicauda Fraser-Brunner 1933
</dwc:scientificName>
<dwc:acceptedNameUsage>Centropyge fisheri (Snyder 1904)
</dwc:acceptedNameUsage>
<dwc:parentNameUsage>Centropyge Kaup, 1860</dwc:parentNameUsage>
<dwc:originalNameUsage>Centropyge flavicauda Fraser-Brunner 1933
</dwc:originalNameUsage>
<dwc:nameAccordingTo>Allen, G.R. 1980. Butterfly and angelfishes of
the world. Volume II. Mergus Publishers. Pp. 149-352.
</dwc:nameAccordingTo>
<dwc:namePublishedIn>Fraser-Brunner, A. 1933. A revision of the
chaetodont fishes of the subfamily Pomacanthinae. Proceedings of the
General Meetings for Scientific Business of the Zoological Society of
London 1933 (pt 3, no.30): 543-599, Pl. 1.</dwc:namePublishedIn>
<dwc:higherClassification>Animalia;Chordata;Vertebrata;Osteichthyes;Actinopterygii;Neopterygii;Teleostei;Acanthopterygii;Perciformes;
Percoidei;Pomacanthidae;Centropyge</dwc:higherClassification>
<dwc:kingdom>Animalia</dwc:kingdom>
<dwc:phylum>Chordata</dwc:phylum>
<dwc:class>Osteichthyes</dwc:class>
<dwc:order>Perciformes</dwc:order>
<dwc:family>Pomacanthidae</dwc:family>
<dwc:genus>Centropyge</dwc:genus>
<dwc:specificEpithet>flavicauda</dwc:specificEpithet>
<dwc:scientificNameAuthorship>Fraser-Brunner 1933
</dwc:scientificNameAuthorship>
<dwc:taxonRank>species</dwc:taxonRank>
<dwc:nomenclaturalCode>ICZN</dwc:nomenclaturalCode>
<dwc:taxonomicStatus>accepted</dwc:taxonomicStatus>
</SimpleDarwinRecord>
</SimpleDarwinRecordSet>
Example of DwC document:

27. Biodiversity Data Representation
Data provisioning
RESTful Web
Services
OBIS
FishBase
SeaLifeBase
GBIF
SpeciesLink
ITIS
…
Web Interfaces
Web Interfaces
Client programs
Usage in
other
applications

28. • E-Infrastructures
• Virtual Research Environments
• The i-Marine Web Portal
• Biodiversity Catalogues
• Management of heterogeneous data
• Tools for Biodiversity data access

29. Remote
Species Products Discovery
Species Products
Discovery allows to
retrieve detailed
information from
several data
providers
We can visualize the occurrence points
on a map and visually detect the errors.
We can inspect the
points metadata

30. Online example:
the i-Marine Species Products Discovery
https://i-marine.d4science.org/group/biodiversitylab/species-data-discovery

31. Biodiversity Data Providers
Remote

32. Species View
Species View allows
to discover species
information from
FishBase
FishBase
Also images and GIS
maps may be
attached to the
species

33. Online example:
the i-Marine Species View
https://i-marine.d4science.org/group/biodiversitylab/species-visualisation