Nicolas Bailly

A Higher Level Classification of All Living Organisms

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.

New Species in the Old World: Europe as a Frontier in Biodiversity Exploration, a Test Bed for 21st Century Taxonomy

The number of described species on the planet is about 1.9 million, with ca. 17,000 new species described annually, mostly from the tropics. However, taxonomy is usually described as a science in crisis, lacking manpower and funding, a politically acknowledged problem known as the Taxonomic Impediment. Using data from the Fauna Europaea database and the Zoological Record, we show that contrary to general belief, developed and heavily-studied parts of the world are important reservoirs of unknown species. In Europe, new species of multicellular terrestrial and freshwater animals are being discovered and named at an unprecedented rate: since the 1950s, more than 770 new species are on average described each year from Europe, which add to the 125,000 terrestrial and freshwater multicellular species already known in this region. There is no sign of having reached a plateau that would allow for the assessment of the magnitude of European biodiversity. More remarkably, over 60% of these new species are described by non-professional taxonomists. Amateurs are recognized as an essential part of the workforce in ecology and astronomy, but the magnitude of non-professional taxonomist contributions to alpha-taxonomy has not been fully realized until now. Our results stress the importance of developing a system that better supports and guides this formidable workforce, as we seek to overcome the Taxonomic Impediment and speed up the process of describing the planetary biodiversity before it is too late.

Fauna Europaea – all European animal species on the web

Abstract Fauna Europaea is Europes main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Retrieving taxa names from large biodiversity data collections using a flexible matching workflow

Abstract In the domain of biological classification there are several taxon name matching services that can search for a species scientific name in a large collection of taxonomic names. Many of these services are available online, and many others run on computers of individual scientists. While these systems may work very well, most suffer from the fact that the list of names used as a reference, and the criteria to decide on a match, are hard-coded in the engine that performs the name matching. In this paper we present BiOnym, a taxon name matching system that separates reference namelists, search criteria and matching engine. The user is offered a choice of several taxonomic reference lists, including the option to upload his/her own list onto the system. Furthermore, BiOnym is a flexible workflow, which embeds and combines techniques using lexical matching algorithms as well as expert knowledge. It is also an open platform allowing developers to contribute with new techniques. In this paper we demonstrate the benefits brought by this approach in terms of the efficiency and effectiveness of the information retrieval process with respect to other solutions.

Introduction to the Greek Taxon Information System (GTIS) in LifeWatchGreece: the construction of the Preliminary Checklists of Species of Greece

The Greek Taxon Information System is an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that is resuming efforts to compile a complete checklist of all species reported from the Greek territory. Such an effort is necessary as a requirement for all signatories of the Convention on Biological Diversity (Greece is a signatory since 1994). Over an estimation published in 2004 according to which 50,000 species are present in Greece, belonging to most kingdoms except bacteria and viruses, a list of 35,000 valid species (and subspecies) has been assembled from previous national and European initiatives and specialized databases on various groups. A new database will be progressively set up in the LifeWatchGreece Infrastructure within the near future. Before the dissemination of this dataset, it is important that the checklists will be validated by specialists for each taxonomic group. The first step already accomplished was to build and publish Preliminary Checklists for some taxonomic groups of marine fauna, which have been validated by specialists on the basis of their expertise and secondary literature. The publication of these Preliminary Checklists is expected to increase the visibility and usability of the database in the future not only to the scientific community but also to the broader domain of biodiversity management, especially in cases where no such checklists have been published yet. The guidelines used to test the first taxonomic groups are presented in this paper. Keywords Biodiversity, global species databases, biodiversity management, data management

Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts quantitative and qualitative properties to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

Using preference-enriched faceted search for species identification

Species identification is essentially a decision-making process comprising steps in which the user makes a selection of characters, figures or photographs, or provides an input, that restricts other choices, until reaching one species. In some identification methods such decisions should have a specific order. Consequently, a wrong decision at the beginning of the process, could exclude a big set of options. To make this process more flexible and less vulnerable to wrong decisions, in this paper we investigate how a Preference-enriched Faceted Search PFS process can be used to aid the identification of species. We show how the proposed process covers and advances the existing methods and we report our experience from applying this process over data taken from FishBase. In the sequent, we elaborate on evaluation and we report the results of a task-based evaluation that shows that the PFS-based method can be used effectively by casual users.

Porifera of Greece: an updated checklist

Abstract Background The checklist of Porifera of Greece was created in the framework of the Greek Taxon Information System (GTIS), an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that has resumed efforts to compile a complete checklist of species recorded from Greece. An updated checklist of Porifera was created on the basis of a list of the Aegean Demospongiae and Homoscleromorpha published one decade ago. All records of species known to occur in Greek waters were taxonomically validated and cross-checked for possible inaccuracies and omissions. Then, all recent publications were reviewed and the species recorded from 2006 to date were added to the list. New information The updated checklist of Porifera of Greece comprises 215 species, classified to 111 genera, 65 families, 24 orders, and 4 classes. In total, 34 new additions were made to the previous species list (8 Calcarea, 17 Demospongiae, 1 Hexactinellida, and 6 Homoscleromorpha) with Calcarea being listed for the first time from the area. The demosponge orders Poecilosclerida, Dictyoceratida, Tetractinellida, Haplosclerida, and Suberitida have the highest number of species covering 62% of the known Greek sponge species richness. It is worth mentioning that 8 species have been first described from Greek waters, 7 of which are considered endemic to this area. Our bibliographic overview also revealed knowledge gaps with regard to specific habitats typically rich in sponge diversity, and marine sectors of Greece.

Species Identification Through Preference-Enriched Faceted Search

There are various ways and corresponding tools that the marine biologist community uses for identifying one species. Species identification is essentially a decision making process comprising steps in which the user makes a selection of characters, figures or photographs, or provides an input that restricts other choices, and so on, until reaching one species. In many cases such decisions should have a specific order, as in the textual dichotomous identification keys. Consequently, if a wrong decision is made at the beginning of the process, it could exclude a big list of options. To make this process more flexible (i.e. independent of the order of selections) and less vulnerable to wrong decisions, in this paper we investigate how an exploratory search process, specifically a Preference-enriched Faceted Search (PFS) process, can be used to aid the identification of species. We show how the proposed process covers and advances the existing methods. Finally, we report our experience from applying this process over data taken from FishBase, the most popular source for marine resources. The proposed approach can be applied over any kind of objects described by a number of attributes.

Ascidiacea (Chordata: Tunicata) of Greece: an updated checklist

Abstract Background The checklist of the ascidian fauna (Tunicata: Ascidiacea) of Greece was compiled within the framework of the Greek Taxon Information System (GTIS), an application of the LifeWatchGreece Research Infrastructure (ESFRI) aiming to produce a complete checklist of species recorded from Greece. This checklist was constructed by updating an existing one with the inclusion of recently published records. All the reported species from Greek waters were taxonomically revised and cross-checked with the Ascidiacea World Database. New information The updated checklist of the class Ascidiacea of Greece comprises 75 species, classified in 33 genera, 12 families, and 3 orders. In total, 8 species have been added to the previous species list (4 Aplousobranchia, 2 Phlebobranchia, and 2 Stolidobranchia). Aplousobranchia was the most speciose order, followed by Stolidobranchia. Most species belonged to the families Didemnidae, Polyclinidae, Pyuridae, Ascidiidae, and Styelidae; these 4 families comprise 76% of the Greek ascidian species richness. The present effort revealed the limited taxonomic research effort devoted to the ascidian fauna of Greece, which is attributed to the lack of experts and low sampling effort. Therefore, major knowledge gaps on the ascidian diversity of Greece occur and further research in this field is needed.