USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 1
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Transcript of USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 1
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
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
Module 1 - Outline
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
e-Infrastructures“e-Infrastructures enable researchers in different locations across the worldto 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/
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.
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
Virtual Research EnvironmentsVirtual 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-InfrastructureVREVRE
VRE
D4ScienceD4Science 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.
A continuously updated list of events / news produced by users and applications
User-shared News
Application-shared News
Share News
D4Science Social
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
D4Science - ResourcesLarge 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 Networkto share opinions and useful news
Algorithms for Biology-related experiments
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
i-Marinei-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
Geospatialstore,
discover, access, and process of geospatial
data
Statisticalexchange
and process of statistical
data
Semanticdiscover and
bridge across
knowledge providers
Physical and chemical features
Inventories of biological
information
Habitat typesSocio-
economic aspects
Marine resource
assessment
Fishery operation,
processingand trade
Marine Planning
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
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.
Biodiversity DataTaxonomies
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
Biodiversity DataOccurrence data
Specimen, Human Observations (direct/indirect)
Records of species presence, usually provided by scientific surveys
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
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
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
<?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 theGeneral Meetings for Scientific Business of the Zoological Society ofLondon 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:
Biodiversity Data RepresentationData provisioning
RESTful Web Services
OBISFishBaseSeaLifeBase
GBIFSpeciesLinkITIS…
Web Interfaces
Web Interfaces
Client programs
Usage in other applications
• E-Infrastructures• Virtual Research Environments• The i-Marine Web Portal• Biodiversity Catalogues• Management of heterogeneous data• Tools for Biodiversity data access
Remote
Species Products DiscoverySpecies 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
Online example: the i-Marine Species Products Discovery
https://i-marine.d4science.org/group/biodiversitylab/species-data-discovery
Species ViewSpecies View allows to discover species information from FishBase
FishBase
Also images and GIS maps may be attached to the species