Search

FloraNER is a distantly supervised named entity recognition dataset (NER). The dataset is built from botanical French literature extracted from the OCR-preprocessed flora of New Caledonia, provided by the National Museum of Natural History in France (MNHN), and distantly annotated with a botanical French corpus created by merging botanical lexicons available online. FloraNER comprises separate sub-datasets for the recognition of plant species names, as well as coarse-grained and fine-grained botanical morphological terms. The resulting datasets are in CSV format, displaying textual data, identified named entities, and their annotations, covering one named entity type "Species" (Espèce in French) for species name identification, two named entity types "Organ" and "Descriptor" for coarse-grained morphological term identification, and eight named entity types for fine-grained morphological term identification: Organ, Descriptor, Form, Color, Development, Structure, Surface, Position, Disposition, and Measure. This dataset can be utilized to train and evaluate named entity recognition models for extracting information from botanical French literature., (© 2024 The Authors.)

Successful bioinspired design depends on practitioners' access to biological data in a relevant form. Although multiple open-access biodiversity databases exist, their presentation is often adapted to life scientists, rather than bioinspired designers. In this paper, we present a new tool, "Bioinspire-Explore", for navigating biodiversity data in order to uncover biological systems of interest for a range of sectors. Bioinspire-Explore allows users to search for inspiring biological models via taxa (species, genera, etc.) as an entry point. It provides information on a taxon's position in the "tree of life", its distribution and climatic niche, as well as its appearance. Bioinspire-Explore also shows users connections in the bioinspiration literature between their taxon of interest and associated biological processes, habitats, and physical measurements by way of their semantic proximity. We believe Bioinspire-Explore has the potential to become an indispensable resource for both biologists and bioinspired designers in different fields.

Zoological nomenclature is the discipline of taxonomy responsible for regulating the scientific names of animal species. It has its roots in Carolus Linnaeus work and has been governed by an international Code since the turn of the 20th century. Its vocabulary, on the other hand, is not always clear. Various authors have established new terminology in order to reduce ambiguity. To make these new terms, but also the classical terms used by the International Code of Zoological Nomenclature, accessible, an electronic thesaurus (link: https://www.loterre.fr/skosmos/FM8/en/) was created, allowing to compare existing terminologies. This thesaurus is also a tool for reflection and discussion, targeting taxonomists and experts in nomenclature.

Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based (OB) occurrences is overthrowing the collection of specimen-based (SB) occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e., SB occurrences) fell from 68% to 18%; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it. Specifically, we emphasize why SB occurrences must be gathered, as a warrant to allow both repeating evolutionary studies and conducting rich and diverse investigations. When impossible to secure, voucher specimens must be replaced with OB occurrences combined with ancillary data (e.g., pictures, recordings, samples, DNA sequences). Ancillary data are instrumental for the usefulness of biodiversity occurrences and we show that, despite improving technologies to collate them, they remain rarely shared. The consequences of such a change are not yet clear but we advocate collecting material evidence or ancillary data to ensure that primary biodiversity data collected lately do not partly become obsolete when doubtful.

An identification key based on French ladybird colouration is proposed for the tribes Chilocorini, Coccinellini, and Epilachnini. These tribes were chosen based on their relatively limited species diversity, as well as their large size and high colour diversity, making them easy to observe and collect. The identification key runs on Xper 3 software, which allows the building of structured knowledge bases and online free-access keys. The online interactive Xper key is available at http://french-ladybird.identificationkey.fr.

Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Background: Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards., Results: The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/., Conclusions: By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

We present a general overview of features and technical specifications of an original interactive key web application for the identification of Chrysochromulina species. The list of species, originally described as belonging in the genus Chrysochromulina, is given and recent taxonomic changes in species and genera of the order Prymnesiales are provided. We briefly discuss the interest of such a key for the identification of phytoplanktonic species.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Single-access keys are a major tool for biologists who need to identify specimens. The construction process of these keys is particularly complex (especially if the input data set is large) so having an automatic single-access key generation tool is essential. As part of the European project ViBRANT, our aim was to develop such a tool as a web service, thus allowing end-users to integrate it directly into their workflow. IKey+generates single-access keys on demand, for single users or research institutions. It receives user input data (using the standard SDD format), accepts several key-generation parameters (affecting the key topology and representation), and supports several output formats. IKey+is freely available (sources and binary packages) at www.identificationkey.fr. Furthermore, it is deployed on our server and can be queried (for testing purposes) through a simple web client also available at www.identificationkey.fr (last accessed 13 August 2012). Finally, a client plugin will be integrated to the Scratchpads biodiversity networking tool (scratchpads.eu).

Background and Methods: The appearance of bluetongue virus (BTV) in 2006 within northern Europe exposed a lack of expertise and resources available across this region to enable the accurate morphological identification of species of Culicoides Latreille biting midges, some of which are the major vectors of this pathogen. This work aims to organise extant Culicoides taxonomic knowledge into a database and to produce an interactive identification key for females of Culicoides in the Western Palaearctic (IIKC: Interactive identification key for Culicoides). We then validated IIKC using a trial carried out by six entomologists based in this region with variable degrees of experience in identifying Culicoides., Results: The current version of the key includes 98 Culicoides species with 10 morphological variants, 61 descriptors and 837 pictures and schemes. Validation was carried out by six entomologists as a blind trial with two users allocated to three classes of expertise (beginner, intermediate and advanced). Slides were identified using a median of seven steps and seven minutes and user confidence in the identification varied from 60% for failed identifications to a maximum of 80% for successful ones. By user class, the beginner group successfully identified 44.6% of slides, the intermediate 56.8% and the advanced 74.3%., Conclusions: Structured as a multi-entry key, IIKC is a powerful database for the morphological identification of female Culicoides from the Western Palaearctic region. First developed for use as an interactive identification key, it was revealed to be a powerful back-up tool for training new taxonomists and to maintain expertise level. The development of tools for arthropod involvement in pathogen transmission will allow clearer insights into the ecology and dynamics of Culicoides and in turn assist in understanding arbovirus epidemiology.

Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide.The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study.

Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms. They have the ability to manage descriptive data and make identifications through interactive keys. They are essential for both authors and users of biodiversity information. Xper(2) version 2.0 is one of the most user-friendly tools in its category and provides a complete environment dedicated to taxonomic management., Availability: Xper(2) software can be freely downloaded at http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2