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PESI
Pan-European Species-directories Infrastructure
European GBIF nodes Meeting — Paris, 4 April 2011
Walter Berendsohn
(based on presentation by Yde de Jong)
PESI project
• Aim: Creating a Pan-European taxonomic backbone (an All-Species Checklist of Europe)
• Based on the existing 3 large European databases:
• + European Fungi (Index Fungorum) & Algae (Algaebase)
• 2.64 million Euro, 40 partners, May 2008 - April 2011
Fauna Europaea
European animal species Terrestrial & freshwater
European Register of Marine Species
European marine species
Euro+Med PlantBase
European plant species Terrestrial & freshwater
PESI in the context of other EU projects
(FP 4) (FP 5) (FP 6) (FP 7)
Digitisation & Infrastructures Integration & e-ScienceNetworks of Excellence
Sustaining Pan-European checklists - issues
Sustaining theexpert networks
Sustaining thedatabasesystems
Sustaining themaintenance (updating)
tools & functions
Sustaining theinteroperability
(e.g. Global Name Architecture)
Sustaining the data dissemination
(webportal)Sustaining the
data verification(quality control / validation) Sustaining the
implementation ofEuropean taxonomic standards
SMEBDSMEBDHost InstitutionsHost Institutions
EDIT Platform for Cybertaxonomy
EDIT Platform for Cybertaxonomy
Focal NetworksFocal Networks
VLIZ / Hosts(LifeWatch?)VLIZ / Hosts(LifeWatch?)
*4Life projects(LifeWatch?)
*4Life projects(LifeWatch?)
Management & CoordinationManagement & Coordination
Infrastructural NetworksC
omm
unit
y N
etw
orks
Zoological Community
Botanical Community
Marine Community
Mycological Community
Expert-networks
Focalpoint
networks
Authorityfiles &
Standards
Datae-Infra-structure
e-Services
Phycological Community
PESI WP2 — Expert Networks
Expert Networks
Society for the Management of Electronic Biodiversity Data(SMEBD)
http://www.smebd.eu
Management & CoordinationManagement & Coordination
Infrastructural NetworksC
omm
unit
y N
etw
orks
Zoological Community
Botanical Community
Marine Community
Mycological Community
Expert-networks
Focalpoint
networks
Authorityfiles &
Standards
Datae-Infra-structure
e-Services
Phycological Community
PESI Focal Points Networks
PESI Focal Point Networks
• Cross-validation pan-European lists with local species lists
– TaxonMatch Tool
• Provide meta-data on local expertise (experts, resources, etc.)
– Focal Points Expertise database
Major tasks of PESI National Focal Points
PESI Validation Tools: Taxon Match Tool - 1
http://www.eu-nomen.eu/portal/taxamatch.phpTAXAMATCH fuzzy matching algorithm by Tony Rees, PHP/MySql port of TAXAMATCH by Michael Giddens, Scientific Names Parser by Dmitry Mozzherin
1. Exact match test
2. Phonetic match test
3. Custom Modified Damerau-Levenshtein Distance (MDLD)
4. Modified n-gram comparison of author names and dates, including known abbreviations
PESI validation tools: Taxon Match Tool - 2
Mapping between two taxon names lists (exact and fussy)
PESI validation tools: Taxon Match Tool - 3
Excel file export
Management & CoordinationManagement & Coordination
Infrastructural NetworksC
omm
unit
y N
etw
orks
Zoological Community
Botanical Community
Marine Community
Mycological Community
Expert-networks
Focalpoint
networks
Authorityfiles &
Standards
Datae-Infra-structure
e-Services
Phycological Community
Taxonomic standards & authority files
• What are the properties of a Taxonomic Backbone
– connecting different uses of the same name for multiple classifications
– persistent name-name relationships of species names
• Optimise data sharing / interoperability
– Linked Data mark-up
– persistent identifiers: globally unique IDs (GUIDs, LSIDs)
– DarwinCore Archive format for transport
• Standardised ontologies / vocabularies
– consensus classification
– consensus distribution and occurence scheme
Conceptual integration
PESI consensus distribution and occurrence scheme
Gazetteer: http://www.vliz.be/vmdcdata/vlimar/
Management & CoordinationManagement & Coordination
Infrastructural NetworksC
omm
unit
y N
etw
orks
Zoological Community
Botanical Community
Marine Community
Mycological Community
Expert-networks
Focalpoint
networks
Authorityfiles &
Standards
Datae-Infra-structure
e-Services
Phycological Community
Taxonomic information e-infrastructure
EDIT Platform dataflow in PESI domain
© Walter Berendsohn
PESI Phyco-Myco databases
Quality control mechanisms
Inconsistency checks used in the merging process
PESI Data Warehouse Model
> 440.000 taxon names~ 210.000 valid species names
> 440.000 taxon names~ 210.000 valid species names
PESI Data Warehouse - statistics
Management & CoordinationManagement & Coordination
Infrastructural NetworksC
omm
unit
y N
etw
orks
Zoological Community
Botanical Community
Marine Community
Mycological Community
Expert-networks
Focalpoint
networks
Authorityfiles &
Standards
Datae-Infra-structure
e-Services
Phycological Community
e-Services for users & dissemination
PESI project website
http://www.eu-nomen.eu/pesi
PESI dataportal
http://www.eu-nomen.eu/portal
Linking to Global Names Architecture
Acknowledgement (PESI SC & management)
Nihat Aktaç
Ward Appeltans
Walter Berendsohn
Phillip Boegh
Louis Boumans
Thierry Bourgoin
Mark Costello
Charles Hussey
Roger Hyam
Yde de Jong
Julia Kouwenberg
David Ouvrad
Henrik Pedersen