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. 2015 Sep 28:(3):e5848.
doi: 10.3897/BDJ.3.e5848. eCollection 2015.

PESI - a taxonomic backbone for Europe

Yde de Jong  1 , Juliana Kouwenberg  2 , Louis Boumans  3 , Charles Hussey  4 , Roger Hyam  5 , Nicola Nicolson  6 , Paul Kirk  6 , Alan Paton  6 , Ellinor Michel  7 , Michael D Guiry  8 , Phillip S Boegh  9 , Henrik Ærenlund Pedersen  10 , Henrik Enghoff  10 , Eckhard von Raab-Straube  11 , Anton Güntsch  11 , Marc Geoffroy  11 , Andreas Müller  11 , Andreas Kohlbecker  11 , Walter Berendsohn  11 , Ward Appeltans  12 , Christos Arvanitidis  13 , Bart Vanhoorne  14 , Joram Declerck  14 , Leen Vandepitte  14 , Francisco Hernandez  14 , Róisín Nash  15 , Mark John Costello  16 , David Ouvrard  7 , Pascale Bezard-Falgas  17 , Thierry Bourgoin  18 , Florian Tobias Wetzel  19 , Falko Glöckler  19 , Günther Korb  19 , Caroline Ring  19 , Gregor Hagedorn  19 , Christoph Häuser  19 , Nihat Aktaç  20 , Ahmet Asan  20 , Adorian Ardelean  21 , Paulo Alexandre Vieira Borges  22 , Dhimiter Dhora  23 , Hasmik Khachatryan  24 , Michael Malicky  25 , Shaig Ibrahimov  26 , Alexander Tuzikov  27 , Aaike De Wever  28 , Snejana Moncheva  29 , Nikolai Spassov  30 , Karel Chobot  31 , Alexi Popov  30 , Igor Boršić  32 , Spyros Sfenthourakis  33 , Urmas Kõljalg  34 , Pertti Uotila  35 , Gargominy Olivier  17 , Jean-Claude Dauvin  36 , David Tarkhnishvili  37 , Giorgi Chaladze  37 , Michael Tuerkay  38 , Anastasios Legakis  39 , László Peregovits  40 , Gudmundur Gudmundsson  41 , Erling Ólafsson  41 , Liam Lysaght  42 , Bella Sarah Galil  43 , Francesco M Raimondo  44 , Gianniantonio Domina  44 , Fabio Stoch  45 , Alessandro Minelli  46 , Voldermars Spungis  47 , Eduardas Budrys  48 , Sergej Olenin  49 , Armand Turpel  50 , Tania Walisch  50 , Vladimir Krpach  51 , Marie Therese Gambin  52 , Laurentia Ungureanu  53 , Gordan Karaman  54 , Roy M J C Kleukers  55 , Elisabeth Stur  56 , Kaare Aagaard  56 , Nils Valland  57 , Toril Loennechen Moen  57 , Wieslaw Bogdanowicz  58 , Piotr Tykarski  59 , Jan Marcin Węsławski  60 , Monika Kędra  60 , Antonio M de Frias Martins  61 , António Domingos Abreu  62 , Ricardo Silva  63 , Sergei Medvedev  64 , Alexander Ryss  64 , Smiljka Šimić  65 , Karol Marhold  66 , Eduard Stloukal  67 , Davorin Tome  68 , Marian A Ramos  69 , Benito Valdés  70 , Francisco Pina  70 , Sven Kullander  71 , Anders Telenius  71 , Yves Gonseth  72 , Pascal Tschudin  72 , Oleksandra Sergeyeva  73 , Volodymyr Vladymyrov  73 , Volodymyr Bohdanovych Rizun  74 , Chris Raper  7 , Dan Lear  75 , Pavel Stoev  76 , Lyubomir Penev  77 , Ana Casino Rubio  78 , Thierry Backeljau  28 , Hannu Saarenmaa  79 , Sandrine Ulenberg  55
Affiliations

PESI - a taxonomic backbone for Europe

Yde de Jong et al. Biodivers Data J. .

Abstract

Background: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New information: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

Keywords: AlgaeBase; Authority File; EU-nomen; EUBON; Euro+Med PlantBase; European Register of Marine Species; European taxonomic backbone; Fauna Europaea; Global Names Architecture; INSPIRE; Index Fungorum; International Plant Names Index (IPNI); LifeWatch; Nomenclature; PESI; Taxonomic indexing; Taxonomy; ZooBank.

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Figures

Figure 1.
Figure 1.
Five community networks (horizontal) are integrated in five categories of coordination effort (vertical) in PESI. Community networks represent the FP4 and FP5 key programs on European taxonomic indexing: Fauna Europaea, ERMS, Euro+Med PlantBase, supplemented by Index Fungorum and AlgaeBase.
Figure 2.
Figure 2.
PESI Expert Communities Common Infrastructure outline, showing a common governance organisation, including relevant expert(ise) network management tools.
Figure 3.
Figure 3.
Europe's integrated taxonomic workforce as established in EDIT and PESI, brought together (as a pilot) into a shared expert system.
Figure 4.
Figure 4.
The Open Source Society network as an analogy for modelling the future Taxonomic Community.
Figure 5.
Figure 5.
PESI Focal Points Network, showing the respective Fauna Europaea, Euro+PlantBase and ERMS focal point partners. Northern African 'proto focal points' are indicated with open circles. Pan-Caucasian Plant Biodiversity Initiative partners are indicated with green asterisks. Focal Points network details are described in Suppl. material 34.
Figure 6.
Figure 6.
The role of PESI Focal Points as an addition to the expert network.
Figure 7.
Figure 7.
Simplified architecture of the EDIT Platform for Cybertaxonomy. Internal data stores are encapsulated by Java and web service APIs.
Figure 8.
Figure 8.
Information flow for merging and publication of checklist data in PESI (after Suppl. material 20).
Figure 9.
Figure 9.
Simplyfied Catalogue of Life Architecture, showing two PESI contributions: Euro-Hub development and governance of EU-based GSD.
Figure 10.
Figure 10.
PESI web-portal homepage (screenshot).
Figure 11.
Figure 11.
PESI web-portal statistics showing the number of unique (monthly) visitors and the number of (monthly) visits since the start of the project (see: Suppl. material 35).
Figure 12.
Figure 12.
PESI web-portal advanced search interface (screenshot).
Figure 13.
Figure 13.
PESI web-portal example of a search and output of all species and infraspecies of molluscs
Figure 14.
Figure 14.
PESI Portal and PESI Datawarehouse (version 3) statistics. Source: http://www.eu-nomen.eu/portal/stats.php.
Figure 15.
Figure 15.
Aspects of increased biodiversity platform interoperability as established in the ViBRANT project (after: Suppl. material 29).
Figure 16.
Figure 16.
Example of virtual lab application (Fauna Europaea VRE pilot), showing the species distribution predictions of Megachile sculpturalis, using the BioVel Portal.
Figure 17.
Figure 17.
Screen capture of a biodiversity dedicated user interface in myBiOSis environment.
Figure 18.
Figure 18.
Screen capture of the Assessment toolkit in myBiOSis environment. This figure demonstrates flexibility of the system to accommodate distinct projects and research scopes.
Figure 19.
Figure 19.
LifeWatch marine virtual research environment (VRE) (source: http://marine.lifewatch.eu).
Figure 20.
Figure 20.
Potential workflows in a next generation linked open-data names architecture.
Figure 21.
Figure 21.
Global Names Architecture schematic representation of three cross-reference layers model.
Figure 22.
Figure 22.
An example ZooBank page (Gasterosteus Saltatrix Linnaeus, 1766), illustrating several GNUB services: (1) user authentication; (2) “fuzzy” searching of GNUB content; (3) APIs and services; (4) ZooBank registration; (5) External Identifier cross-linking; (6) BHL page linking; (7) similar/related name discovery (via GNI’s name searching service); and (8) multi-lingual support. Not shown are services to manage user accounts, de-duplicate records, prototype reconciliation tools, services for journal publishers, and visualization tools for author publication history and other statistics.
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