BACKGROUND:The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS:To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS:Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

Geometric morphometric analyses are used to explore variation of maxillary dental arcades of Australopithecus afarensis, expanding on the work of Hanegraef and Spoor, 2025 (Morphological variation of the Australopithecus afarensis maxilla. Journal of Human Evolution, 201, 103651) by integrating evidence from a large sample of virtually reconstructed mandibles. Size and shape of maxillary dental arcades can be predicted accurately from mandibular landmarks based on strong covariation between occluding upper and lower dentitions, and a novel method was developed to correct for reduced shape variation in these predictions. As predictions are restricted to the alveolar process, morphological information about the rest of the maxilla is lost. The trade-off between a smaller sample with comprehensive morphology and a larger sample with restricted morphology is discussed. Here, we analyzed 9 original and 17 predicted A. afarensis dental arcades in the comparative context of 448 extant hominine (modern human and African ape) maxillae. This study found that (1) degrees of size and shape variation are high in A. afarensis, potentially even higher than in Gorilla species when including the predictions in the fossil sample, (2) no allometry was detected, even when expanding the A. afarensis sample with predictions, (3) size and shape do not significantly change over time when analyzing original and predicted A. afarensis dental arcades together, and (4) sexual form and shape dimorphism, but not sexual size differences, are reduced when including A. afarensis predictions in the fossil sample. Our results quantifying the range and pattern of variation of the A. afarensis maxilla provide a comparative context when assessing whether or not other Plio-Pleistocene hominin specimens are conspecific.

This study presents a framework to automatically analyse head motion in birds from videos of natural behaviours. The process involves detecting birds, identifying key points on their heads and tracking changes in their positions over time. Bird detection and key point extraction were trained on publicly available datasets, featuring videos and images of diverse bird species in uncontrolled settings. Initial challenges with complex video backgrounds causing misidentifications and inaccurate key points were addressed through validation, refinement, filtering and smoothing. Head angular velocities and rotation frequencies were computed from the refined key points. The algorithm performed well at moderate speeds but was limited by the 30 Hz frame rate of most videos, which constrained measurable angular velocities and frequencies and caused motion blur, affecting key point detection. Our findings suggest that the framework may provide plausible estimates of head motion but also emphasize the importance of high frame-rate videos in future research, including extensive comparisons against ground truth data, to fully characterize bird head movements. Importantly, this work is a foundational effort to understand the evolutionary drivers of the semicircular canals, the biosensor that monitors head rotations, for both extinct and extant tetrapods.

Experiments with high-risk pathogens are routinely conducted under strict conditions of biosafety and biosecurity. In this Comment, we propose a Minimum Information about a High Containment Laboratory Experiment (MIHCLE) reporting standard. Although conceived particularly for work in biosafety level (BSL) 4 laboratories, it can be generally applicable to any research performed in both high (BSL-3) and maximum (BSL-4) containment facilities.

Background Descriptive metadata are vital for reporting, discovering, leveraging, and mobilizing research datasets. However, resolving metadata issues as part of a data management plan can be complex for data producers. To organize and document data, various descriptive metadata must be created. Furthermore, when sharing data, it is important to ensure metadata interoperability in line with FAIR (Findable, Accessible, Interoperable, Reusable) principles. Given the practical nature of these challenges, there is a need for management tools that can assist data managers effectively. Additionally, these tools should meet the needs of data producers and be user-friendly, requiring minimal training.Results We developed Maggot (Metadata Aggregation on Data Storage), a web-based tool to locally manage a data catalog using high-level metadata. The main goal was to facilitate easy data dissemination and deposition in data repositories. With Maggot, users can easily generate and attach high-level metadata to datasets, allowing for seamless sharing in a collaborative environment. This approach aligns with many data management plans as it effectively addresses challenges related to data organization, documentation, storage, and the sharing of metadata based on FAIR principles within and beyond the collaborative group. Furthermore, Maggot enables metadata crosswalks (i.e., generated metadata can be converted to the schema used by a specific data repository or be exported using a format suitable for data collection by third-party applications).Conclusion The primary purpose of Maggot is to streamline the collection of high-level metadata using carefully chosen schemas and standards. Additionally, it simplifies data accessibility via metadata, typically a requirement for publicly funded projects. As a result, Maggot can be utilized to promote effective local management with the goal of facilitating data sharing while adhering to the FAIR principles. Furthermore, it can contribute to the preparation of the future EOSC FAIR Web of Data within the European Open Science Cloud framework.

How the intricate mammalian cochlea evolved, and its functional implications, remain only partly understood. Here, we explore cochlear morphology across 101 extant and fossil species of the mammalian grand order Euarchonta using micro-computed tomography, three-dimensional geometric morphometrics and phylogenetic comparative analyses. We find substantial shape variation across taxa, likely driven by an interplay between evolutionary history, morphological constraints and potentially functional demands, although these remain difficult to interpret. Evolutionary models suggest the rate of cochlear shape evolution was heterogeneous, with some lineages showing particularly high rates, likely linked with adaptive selection pressures (e.g. tarsiers, Cercopithecus). Ancestral state reconstructions reveal lemuriforms retain the ancestral strepsirrhine cochlear shape—conical with around 2½ turns—while lorisiforms exhibit a derived cylindrical cochlea with increased coiling. The highly coiled cochlea of tarsiers reflects cranial constraints and functional demands, particularly for high-frequency hearing. In anthropoids, platyrrhines nest within catarrhine variation. Among the latter, cercopithecins trend towards increased coiling, whereas colobines and hominoids retain less coiled shapes. Finally, while body size has little effect on cochlear shape, its interaction with cochlear length predicts the number of turns, supporting the theory that cochlear coiling enabled the development of a longer basilar membrane within a small petrous space.

Open Science Clusters’ Action for Research and Society (OSCARS) is a EU-funded project that will bring your research data to new audiences and target new use-cases. The FAIR (Findable, Accessible, Interoperable and Reusable) principles allow research data to be used in new and novel ways, with increased citations acknowledging the original researchers and facilities. OSCARS builds on the EOSC (European Open-Science Cloud) science cluster’s outcomes to support open science, by enhancing communication between the science clusters, creating thematic competence centres, improving the outcomes of the science clusters software and services, connecting this activity with other EOSC funded activities, and providing direct funding for open science projects.

Hypercanines, or hypertrophied canines, are observed in a wide range of both extinct and extant synapsids. In non-mammaliaform cynodonts, the Permo-Triassic forerunners of mammals, long canines are not uncommon, appearing in several unrelated taxa within the clade. Among them is Trucidocynodon riograndensis , a carnivorous ecteniniid cynodont from the Late Triassic of Brazil, which exhibits a specialized dentition, including spear-shaped incisors, very long and narrow canines, and sectorial postcanines with distally oriented cusps, all of which have finely serrated margins. Recent synchrotron X-ray micro-computed tomography of a large specimen (CAPPA/UFSM 0029; Várzea do Agudo site, Brazil) provides new insights into its lower jaw and dentition, as well as offers the first digital endocast of an ecteniniid. Our study reveals the presence of (i) putatively opened-root canines in the adult stage and the possible presence of unresorbed remnant of an old canine, which may indicate that the specimen stopped replacing its canines; (ii) lower canines that are longer than the upper canines and, in occlusion, were kept inside deep paracanine fossae that perforated the dorsal surface of the rostrum; (iii) a diastema between the incisors and lower canine, which is absent in the holotype; (iv) advanced brain structures, such as the absence of a pineal body, presence of cerebral hemispheres divided by the interhemispheric sulcus and expanded laterally, and a higher encephalization quotient than non-mammaliaform prozostrodonts, reflecting the homoplastic evolution of relative brain sizes observed in Triassic cynodont lineages. Finally, the abundance of carnivorous and omnivorous species at the Várzea do Agudo site, where the specimen was found—including the archosauriforms Dynamosuchus collisensis and Stenoscelida aurantiacus —suggests a diverse predator guild that warrants further investigation from a paleoecological perspective.

ABSTRACT This paper provides a pioneering study case on monitoring fish biodiversity in ports through the eDNA and citizen science approach. eDNA samples were collected in the spring and in fall 2022 in the ports of Calvi, L'Île‐Rousse, STARESO, Saint‐Florent. Samples collected led to the identification of 73 taxa. These ports appeared to harbor at least 20% of the known teleost biodiversity in Corsica and 11% of the Mediterranean teleost biodiversity. The ports of Calvi and L'Île‐Rousse displayed the highest taxonomic, phylogenetic, and functional diversities and appeared the most similar. However, taxonomic turnover highlighted that none of the 4 ports was a subset of any of the others. In August 2022, an extreme climate event (ECE) struck Corsica, offering a unique opportunity to collect data under abnormal conditions. Although it is not possible to distinguish the seasonal effect from the ECE effect in the fall, we detected in all ports but Saint‐Florent an increase in taxonomic richness, phylogenetic, and functional diversity: we did not only detect new species but also showed that these species led to an increase in the local representativeness of phylogenetic diversity, most likely correlated with new functional traits. The port of Saint‐Florent displayed the highest relative phylogenetic diversity, that is, a smaller but evolutionarily more distinct group of species. Our study demonstrated the robustness and relevance of eDNA citizen science coupled with relevant indicators for port biodiversity monitoring and emphasized the need for more research and targeted conservation efforts to better understand and mitigate the ecological impacts of ports while exploring their potential as habitats.

Background: Descriptive metadata are crucial for the discovery, reporting and mobilisation of research datasets. Addressing all metadata issues within the Data Management Plan often poses challenges for data producers. Organising and documenting data within data storage entails creating various descriptive metadata. Subsequently, data sharing involves ensuring metadata interoperability in alignment with FAIR principles. Given the tangible nature of these challenges, a real need for management tools has to be addressed to assist data managers to the fullest extent. Moreover, these tools have to meet data producers requirements and be user-friendly as well with minimal training as prerequisites. Results: We developed Maggot which stands for Metadata Aggregation on Data Storage, specifically designed to annotate datasets by generating metadata files to be linked into storage spaces. Maggot enables users to seamlessly generate and attach comprehensible metadata to datasets within a collaborative environment. This approach seamlessly integrates into a data management plan, effectively tackling challenges related to data organisation, documentation, storage, and frictionless FAIR metadata sharing within the collaborative group and beyond. Furthermore, for enabling metadata crosswalk, metadata generated with Maggot can be converted for a specific data repository or configured to be exported into a suitable format for data harvesting by third-party applications. Conclusion: The primary feature of Maggot is to ease metadata capture based on a carefully selected schema and standards. Then, it greatly eases access to data through metadata as requested nowadays in projects funded by public institutions and entities such as Europe Commission. Thus, Maggot can be used on one hand to promote good local versus global data management with open data sharing in mind while respecting FAIR principles, and on the other hand to prepare the future EOSC FAIR Web of Data within the framework of the European Open Science Cloud.

The human otolithic system (utricle and saccule), housed within the bony vestibule of the inner ear, establishes our sense of balance in conjunction with the semicircular canals. Yet, while the morphological evolution of the semicircular canals is actively explored, comparative morphological analyses of the otolithic system are lacking. This is regrettable because functional links with head orientation suggest the otolithic system could be used to track postural change throughout human evolution and across primates more broadly. In this context, we present the first analysis of the evolution of the human otolithic system within an anthropoid primate setting. Using the vestibule as a morphological proxy for the utricle and saccule, we compare humans to 13 other extant anthropoid species, and use phylogenetically-informed methods to find correlations with body size, endocranial flexion, and head-neck posture. Our results, obtained through micro-CT of 136 inner ears, reveal two major evolutionary transitions in hominoids, leading to distinctive vestibular morphology in humans, characterized by otolithic morphology resembling squirrel monkeys (possibly due to reversal), with a pronounced supraovalic fossa. Finally, we find a positional signal embedded in the anthropoid bony vestibule, providing the foundation to further explore the evolution of human head-neck posture using inner ear morphology. Morphometric modeling reveals evolutionary divergences of the otolithic inner ear in humans and apes, with a possible link to the evolution of postural behavior.

This study introduces a framework applicable to videos of habitual behaviors of multiple bird species to automatically assess head angular velocities and frequencies during various behaviors in natural habitats. The process involves detecting birds, identifying key points on their heads, and tracking changes in their positions over time. Bird detection and key point extraction were trained on publicly available datasets, including Animal Kingdom, NABirds, Birdsnap, CUB-200-2011, and eBird, featuring videos and images of diverse bird species in uncontrolled settings. Initial challenges arose due to the complexity of video backgrounds, leading to misidentifications and inaccurate key point estimates. These issues were addressed through validation, refinement, filtering, and smoothing steps. Head angular velocities and rotation frequencies were computed from the refined key points. The algorithm performed well at moderate speeds but was limited by the 30 Hz frame rate of most eBird videos, which constrained measurable angular velocities and frequencies and caused motion blur, affecting key point detection. Our findings suggest that the framework may provide plausible estimates of head motion but also emphasize the importance of high frame rate videos in future research, including extensive comparisons against ground truth data, to fully characterize bird head movements. ### Competing Interest Statement The authors have declared no competing interest.

Environmental challenges are rarely confined to national, disciplinary, or linguistic domains. Convergent solutions require international collaboration and equitable access to new technologies and practices. The ability of international, multidisciplinary and multilingual research teams to work effectively can be challenging. A major impediment to innovation in diverse teams often stems from different understandings of the terminology used. These can vary greatly according to the cultural and disciplinary backgrounds of the team members. In this paper we take an empirical approach to examine sources of terminological confusion and their effect in a technically innovative, multidisciplinary, multinational, and multilingual research project, adhering to Open Science principles. We use guided reflection of participant experience in two contrasting teams-one applying Deep Learning (Artificial Intelligence) techniques, the other developing guidance for Open Science practices-to identify and classify the terminological obstacles encountered and reflect on their impact. Several types of terminological incongruities were identified, including fuzziness in language, disciplinary differences and multiple terms for a single meaning. A novel or technical term did not always exist in all domains, or if known, was not fully understood or adopted. Practical matters of international data collection and comparison included an unanticipated need to incorporate different types of data labels from country to country, authority to authority. Sometimes these incongruities could be solved quickly, sometimes they stopped the workflow. Active collaboration and mutual trust across the team enhanced workflows, as incompatibilities were resolved more speedily than otherwise. Based on the research experience described in this paper, we make six recommendations accompanied by suggestions for their implementation to improve the success of similar multinational, multilingual and multidisciplinary projects. These recommendations are conceptual drawing on a singular experience and remain to be sources for discussion and testing by others embarking on their research journey.

Biomedical data are generated and collected from various sources, including medical imaging, laboratory tests and genome sequencing. Sharing these data for research can help address unmet health needs, contribute to scientific breakthroughs, accelerate the development of more effective treatments and inform public health policy. Due to the potential sensitivity of such data, however, privacy concerns have led to policies that restrict data sharing. In addition, sharing sensitive data requires a secure and robust infrastructure with appropriate storage solutions. Here, we examine and compare the centralized and federated data sharing models through the prism of five large-scale and real-world use cases of strategic significance within the European data sharing landscape: the French Health Data Hub, the BBMRI-ERIC Colorectal Cancer Cohort, the federated European Genome-phenome Archive, the Observational Medical Outcomes Partnership/OHDSI network and the EBRAINS Medical Informatics Platform. Our analysis indicates that centralized models facilitate data linkage, harmonization and interoperability, while federated models facilitate scaling up and legal compliance, as the data typically reside on the data generator's premises, allowing for better control of how data are shared. This comparative study thus offers guidance on the selection of the most appropriate sharing strategy for sensitive datasets and provides key insights for informed decision-making in data sharing efforts.

Endothermy underpins the ecological dominance of mammals and birds in diverse environmental settings1,2. However, it is unclear when this crucial feature emerged during mammalian evolutionary history, as most of the fossil evidence is ambiguous3–17. Here we show that this key evolutionary transition can be investigated using the morphology of the endolymph-filled semicircular ducts of the inner ear, which monitor head rotations and are essential for motor coordination, navigation and spatial awareness18–22. Increased body temperatures during the ectotherm–endotherm transition of mammal ancestors would decrease endolymph viscosity, negatively affecting semicircular duct biomechanics23,24, while simultaneously increasing behavioural activity25,26 probably required improved performance27. Morphological changes to the membranous ducts and enclosing bony canals would have been necessary to maintain optimal functionality during this transition. To track these morphofunctional changes in 56 extinct synapsid species, we developed the thermo-motility index, a proxy based on bony canal morphology. The results suggest that endothermy evolved abruptly during the Late Triassic period in Mammaliamorpha, correlated with a sharp increase in body temperature (5–9 °C) and an expansion of aerobic and anaerobic capacities. Contrary to previous suggestions3–14, all stem mammaliamorphs were most probably ectotherms. Endothermy, as a crucial physiological characteristic, joins other distinctive mammalian features that arose during this period of climatic instability28. The functional morphology of the fluid-filled semicircular ducts of the inner ear is adapted to body temperature and behavioural activity and can be used to investigate the evolution of endothermy.

Although FAIR Research Data Principles are targeted at and implemented by different communities, research disciplines, and research stakeholders (data stewards, curators, etc.), there is no conclusive way to determine the level of FAIRness intended or required to make research artefacts (including, but not limited to, research data) Findable, Accessible, Interoperable, and Reusable. The FAIR Principles cover all types of digital objects, metadata, and infrastructures. However, they focus their narrative on data features that support their reusability. FAIR defines principles, not standards, and therefore they do not propose a mechanism to achieve the behaviours they describe in an attempt to be technology/implementation neutral. Various FAIR assessment metrics and tools have been designed to measure FAIRness. Unfortunately, the same digital objects assessed by different tools often exhibit widely different outcomes because of these independent interpretations of FAIR. This results in confusion among the publishers, the funders, and the users of digital research objects. Moreover, in the absence of a standard and transparent definition of what constitutes FAIR behaviours, there is a temptation to define existing approaches as being FAIR-compliant rather than having FAIR define the expected behaviours. This whitepaper identifies three high-level stakeholder categories -FAIR decision and policymakers, FAIR custodians, and FAIR practitioners - and provides examples outlining specific stakeholders' (hypothetical but anticipated) needs. It also examines possible models for governance based on the existing peer efforts, standardisation bodies, and other ways to acknowledge specifications and potential benefits. This whitepaper can serve as a starting point to foster an open discussion around FAIRness governance and the mechanism(s) that could be used to implement it, to be trusted, broadly representative, appropriately scoped, and sustainable. We invite engagement in this conversation in an open Google Group fair-assessment-governance@googlegroups.com

Reliable quantitative vegetation reconstructions for Europe during the Holocene are crucial to improving our understanding of landscape dynamics, making it possible to assess the past effects of environmental variables and land-use change on ecosystems and biodiversity, and mitigating their effects in the future. We present here the most spatially extensive and temporally continuous pollen-based reconstructions of plant cover in Europe (at a spatial resolution of 1° × 1°) over the Holocene (last 11.7 ka BP) using the ‘Regional Estimates of VEgetation Abundance from Large Sites’ (REVEALS) model. This study has three main aims. First, to present the most accurate and reliable generation of REVEALS reconstructions across Europe so far. This has been achieved by including a larger number of pollen records compared to former analyses, in particular from the Mediterranean area. Second, to discuss methodological issues in the quantification of past land cover by using alternative datasets of relative pollen productivities (RPPs), one of the key input parameters of REVEALS, to test model sensitivity. Finally, to validate our reconstructions with the global forest change dataset. The results suggest that the RPPs.st1 (31 taxa) dataset is best suited to producing regional vegetation cover estimates for Europe. These reconstructions offer a long-term perspective providing unique possibilities to explore spatial-temporal changes in past land cover and biodiversity.