TAXREF-LD: A Reference Thesaurus for Biodiversity on the Web of Linked Data

International audienc

A Model to Represent Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF

International audienceTaxonomic registers are key tools to help us comprehend the diversity of nature. Publishing such registers in the Web of Data, following the standards and best practices of Linked Open Data (LOD), is a way of integrating multiple data sources into a world-scale, biological knowledge base. In this paper, we present an ongoing work aimed at the publication of TAXREF, the French national taxonomic register, on the Web of Data. Far beyond the mere translation of the TAXREF database into LOD standards, we show that the key point of this endeavor is the design of a model capable of capturing the two coexisting yet distinct realities underlying taxonomic registers, namely the nomenclature (the rules for naming biological entities) and the taxonomy (the description and characterization of these biological entities). We first analyze different modelling choices made to represent some international taxonomic registers as LOD, and we underline the issues that arise from these differences. Then, we propose a model aimed to tackle these issues. This model separates nomenclature from taxonomy, it is flexible enough to accommodate the ever-changing scientific consensus on taxonomy, and it adheres to the philosophy underpinning the Semantic Web standards. Finally, using the example of TAXREF, we show that the model enables interlinking with third-party LOD data sets, may they represent nomenclatural or taxonomic information

Assisting Biologists in Editing Taxonomic Information by Confronting Multiple Data Sources using Linked Data Standards

International audienc

Construction du référentiel taxonomique commun TAXREF, socle pour la connaissance et l'échange de données

National audienceUne des missions du Muséum national d’Histoire naturelle (MNHN) est d’établir une synthèse de la biodiversité et du patrimoine naturel français. Dans ce contexte, il est en charge de l’élaboration du référentiel taxonomique pour la faune, la flore et la fonge, TAXREF. Ce référentiel unique liste et organise les noms scientifiques de l'ensemble des êtres vivants recensés sur les territoires français, métropole et outremer, et constitue la pierre angulaire du Système d’Information sur la Nature et les Paysages (SINP). Il est utilisé par de nombreux acteurs publics, privés et de la société civile (collectivités, conservateurs, aménageurs, enseignants, citoyens, etc.). TAXREF est de plus aligné avec d'autres référentiels taxonomiques ou nomenclaturaux internationaux.Dans cette présentation, nous aborderons les méthodes d'élaboration d'un tel référentiel, basées sur les codes de nomenclature, un modèle de données, des ressources bibliographiques et la constitution d'un réseau d'experts locaux, nationaux et internationaux, ainsi que les procédures de contrôles qui visent à parfaire un référentiel complexe de quelques 500.000 items. Nous présenterons les résultats et la stratégie d'acquisition. Nous aborderons également la Base de connaissance des espèces qui lui est liée : espèces protégées, menacées, mais également les interactions entre espèces qui proposent une vision dynamique de la biodiversité au delà de la simple approche descriptive.Un tel référentiel n'est utile que s'il est largement exploité. Nous décrirons donc les différentes mises à disposition de ce référentiel : outils de réconciliation, webservice TAXREF et webservice pour les statuts (base de connaissance). En particulier, nous décrirons la modélisation d’un thésaurus exprimé en SKOS (Simple Knowledge Organisation System) afin de produire une version de TAXREF exploitable avec les technologies du web sémantique. Nous aborderons la question du lien entre ce « TAXREF-SKOS » et d’autres thésaurus et ontologies existantes. Enfin, nous décrirons le travail en cours visant à l'exposer sur le web de données sous forme d’URI pérennes déréférençables (Linked Data)

Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities

As the biodiversity community increasingly adopts Semantic Web (SW) standards to represent taxonomic registers, trait banks or museum collections, some questions come up relentlessly: How to model the data? For what goals? Can the same model fulfill different goals? So far, the community has mostly considered the SW standards through their most salient manifestation: the Web of Linked Data (Heath and Bizer 2011). Indeed, the 5-star Linked Data principles are geared towards the building of a large, distributed knowledge graph that may successfully fulfill biodiversity’s need for interoperability and data integration. However, the SW addresses a much broader set of problems involving automatic reasoning. For instance, reasoners can exploit ontological knowledge to improve query answering, leverage class definitions to infer class subsumption relationships, or classify individuals i.e. compute instance relationships between individuals and classes by applying reasoning techniques on class definitions and instance descriptions (Shearer et al. 2008). Whether a "thing" should be modelled as a class or a class instance has been debated at length in the SW community, and the answer is often a matter of perspective. In the context of taxonomic registers for example, the NCBI Organismal Classification (Federhen 2012) and Vertebrate Taxonomy Ontology (Midford et al. 2013) represent taxa as classes in the Ontology Web Language (OWL). By contrast, other initiatives represent taxa as instances of various classes, e.g. the SKOS Concept class (skos:Concept) in the AGROVOC thesaurus (Caracciolo et al. 2013) (we speak of the instances as SKOS concepts), the Darwin Core taxon class (dwc:Taxon) in Encyclopedia of Life (Parr et al. 2016), or classes depicting taxonomic ranks in GeoSpecies, DBpedia and the BBC Wildlife Ontology. Such modelling discrepancies impede linking congruent taxa throughout taxonomic registers. Indeed, one can state the equivalence between two classes (with owl:equivalentClass) or two class instances (with owl:sameAs, skos:exactMatch, etc.), but good practices discourage the alignment of classes with class instances (Baader et al. 2003). Recently, Darwin Core's popularity has fostered the modeling of taxa as instances of class dwc:Taxon (Senderov et al. 2018, Parr et al. 2016). In this context, pragmatism may incline a Linked Data provider to comply with this majority trend to ensure maximum interlinking. Although technically and conceptually valid, this choice entails certain drawbacks. First, considering a taxon only as a an instance misses the fact that it is a set of biological individuals with common characteristics. An OWL class exactly captures this semantics through the set of necessary and sufficient conditions that an individual must meet to be a class member. In turn, an OWL reasoner can leverage this knowledge to perform query answering, compute subsumption or instance relationships. By contrast, taxa depicted by class instances are not defined but described by stating their properties. Hence the second drawback: unless we develop bespoke reasoners, there is not much a standard OWL reasoner can deduce from instances. Yet, some works have demonstrated the effectiveness of logic representation and reasoning capabilities, e.g. computing the alignments of two primate classifications (Franz et al. 2016) using generic reasoners that nevertheless require proprietary input formats. OWL reasoners are typically designed to solve such classification problems. They may leverage taxonomic ontologies to compute alignments with other ontologies or apply reasoning to individuals' properties to infer their species. Hence, pragmatically following the instance-based approach may indeed maximize interlinking in the short term, but bears the risk of denying ourselves potentially desirable use cases in the longer term. We believe that developing class-based ontologies for biodiversity should help leverage the SW’s extensive theoretical and practical works to tackle a variety of use cases that so far have been addressed with bespoke solutions

Inventaire des poissons de l’archipel de Saint-Pierre et Miquelon

International audienceA list of diadromous and marine fishes occurring in the Saint-Pierre and Miquelon archipelago and its eez has been compiled from various available data sources: collections, local and international databases, and literature. this belated work was needed as the only existing checklist dates back to the 19th century and Fishbase, as of early 2022, provided a list of only 14 species, and 81 in the French taxonomic register taXreF. The list assembled here covers 122 species, of which 111 are marine fishes, assigned to 103 genera and 66 families. This list is not comprehensive, but it constitutes a first reference, to be updated with new information.Une liste des poissons diadromes et marins de l’archipel de Saint-Pierre et miquelon et sa zee a été constituée à partir des différentes sources de données disponibles : collections, base de données locales et internationales, et bibliographie. ce travail était nécessaire car l’unique inventaire existant remonte au x i x e siècle et Fishbase au début de 2022, fournissait une liste de seulement 14 espèces, et 81 dans le référentiel taxonomique français taXreF. la présente liste contient 122 espèces, dont 111 marines, réparties en 103 genres et 66 familles. cette liste n’est pas exhaustive et constitue une première référence, qui pourra être mise à jour avec de nouvelles connaissances

Inventaire des poissons de l’archipel de Saint-Pierre et Miquelon

International audienceA list of diadromous and marine fishes occurring in the Saint-Pierre and Miquelon archipelago and its eez has been compiled from various available data sources: collections, local and international databases, and literature. this belated work was needed as the only existing checklist dates back to the 19th century and Fishbase, as of early 2022, provided a list of only 14 species, and 81 in the French taxonomic register taXreF. The list assembled here covers 122 species, of which 111 are marine fishes, assigned to 103 genera and 66 families. This list is not comprehensive, but it constitutes a first reference, to be updated with new information.Une liste des poissons diadromes et marins de l’archipel de Saint-Pierre et miquelon et sa zee a été constituée à partir des différentes sources de données disponibles : collections, base de données locales et internationales, et bibliographie. ce travail était nécessaire car l’unique inventaire existant remonte au x i x e siècle et Fishbase au début de 2022, fournissait une liste de seulement 14 espèces, et 81 dans le référentiel taxonomique français taXreF. la présente liste contient 122 espèces, dont 111 marines, réparties en 103 genres et 66 familles. cette liste n’est pas exhaustive et constitue une première référence, qui pourra être mise à jour avec de nouvelles connaissances

Knowledge Base on Species Life Traits : A Spanish/French Plinian Core implementation use case

International audienceThe French “Traits” working group was created in 2021 to support the development of the national knowledge base on species life traits managed by the PatriNat department*1, to identify and implement a suitable standard for managing and sharing species life traits (including interactions) at the national, then international, level. Its core members are part of several PatriNat teams (Species Knowledge, Dissemination & Mediation, Coordination of Information Systems), as well as other French research units*2 working on the topic of traits and ontologies. The Plinian Core (Plinian Core Task Group 2021) was first discussed in 2004 and its development began in 2005–2006 when the first version was deployed as a collaboration between InBIO*3 (Costa Rica) and GBIF Spain*4. It reuses and extends the Darwin Core vocabulary (Wieczorek et al. 2012, Darwin Core Maintenance Interest Group 2014) to describe different aspects of biological species information, that is, all kinds of properties or traits related to taxa, including biological and non-biological species traits. The Plinian Core was discussed with Dr Pando (convener of the TDWG Plinian Core Task Group*5) during one of the Traits working group meetings, and was found to be relevant to the French species life traits database (currently in development). The Traits working group future works will be following the example of the Plinian Core-based EIDOS database*6 (Spanish Ministry for the Ecological Transition), which allows for detailed species pages with distinct information sections (e.g., interactions, taxonomy, legal status, conservation). This collaboration resulted in a Capacity Enhancement Support Programme project submission (GBIF 2023) between French and Spanish partners, allowing for the consolidation of both the infrastructure and the sharing process of species life traits for taxa found on all French territories, as well as European Union territories. Additionally, this is an opportunity to provide information to GBIF (Global Biodiversity Information Facility) through a new update of the TAXREF (Gargominy 2022) national checklist, one of the core constituents of the GBIF Backbone Taxonomy (GBIF 2022). Species life traits and interactions will be added thanks to the new Plinian Core extension implemented on the GBIF Integrated Publishing Toolkit (IPT),*7 and an Atlas of Living Australia’s architecture BIE (Biodiversity Information Explorer) module*8 developed by Costa Rica in the context of a Capacity Enhancement Support Programme (CESP) project carried out with SIBBR*9 (GBIF Brasil)

An assessment of the endemic spermatophytes, pteridophytes and bryophytes of the French Overseas Territories: towards a better conservation outlook

International audienceA broad range of climatic and biogeographical conditions are represented in the French Overseas Territories, from sub-polar to equatorial, resulting in a high diversity of endemic species. We mobilized data from herbaria, floras, checklists, literature, the expertise of botanists and plant ecologists to compile the most complete dataset on endemic vascular plants and bryophytes in the 15 French Overseas Territories. To date, 3748 spermatophytes (seed plants), 244 pteridophytes (ferns and lycophytes) and 448 bryophytes are strictly endemic to the overseas territories. New Caledonia, French Polynesia and Réunion harbour the highest numbers of strictly endemic species, yet French Guiana and the French Antilles harbour high numbers of regional endemic species due to their proximity with other territories. The endemic flora of these territories is highly threatened. In particular, 51% of strictly endemic spermatophytes are threatened and many species at risk belong to Rubiaceae and Orchidaceae families. Around 82% and 69% of strict and regional endemic spermatophytes and pteridophytes are found in the Paris herbaria. Only 34% of endemic bryophytes have their label information fully databased so that their total number in Paris herbaria is not known. Databasing the remaining specimens in the collection will greatly enhance future research and conservation projects. To facilitate the use of the information we compiled, we provide a publicly searchable dataset of the checklist. This study not only provides a picture of the flora of French overseas territories; it also identifies gaps in knowledge on which future research efforts in systematics, ecology and conservation could focus

Pre-assessments of plant conservation status in islands: the case of French Overseas Territories

International audienceAssessment methods have been developed to estimate a preliminary conservation status for species and subsequently to facilitate the building of Red Lists. Such pre-assessment methods could be particularly useful in the French Overseas Territories (FOTs) where Red Lists tend to be outdated or absent and where a high number of endemic species face detrimental anthropogenic pressures. We first aimed to conduct a preliminary assessment (hereafter, pre-assessment) of the conservation status of endemic plants from Guadeloupe, Martinique, Réunion, Mayotte, French sub-Antarctic islands, New Caledonia, and Scattered Islands. We then compared the various methods used in conducting the pre-assessment and discussed ways to adapt these methods to small territories. We compiled occurrence data of endemic species identified thanks to a previous taxonomic work and pre-assessed their conservation status under Red List criteria A and B and the use of a Random Forest algorithm. We then measured the accuracy, specificity, and sensitivity of each method based on existing Red Lists. The Random Forest algorithm and a method based on range-size performed best at correctly attributing conservation status. Using these pre-assessment methods, we estimated that up to 60% of the endemic flora of the FOTs is potentially threatened. Range restriction but also anthropogenic pressures were key factors that explained these risks. Pre-assessment methods are useful tools to get a first measure of species conservation status. These methods should be adapted to the territories considered and their conservation issues in order to reach a good performance