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Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research. ispartof: DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION vol:2019 ispartof: location:England status: published

To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia).

The information provided here represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and sampling, data integration, and modelling) that are typical for generating EBVs. Recognising the potential value of those EBV templates for European biodiversity monitoring, our objective is to share them for enhancing transparency, knowledge exchange and collaboration, and promoting the operationalisation of EBVs across Europe. EuropaBON (https://europabon.org/) is a Horizon 2020 research and innovation action funded by the European Commission that seeks to co-design a European Biodiversity Observation Network. This network aims to bridge the gap between the biodiversity data needs of policy-makers and authorities on the one hand and the existing reporting streams and available data sources on the other hand, considering both present obligations and forthcoming policy needs. Essential Biodiversity Variables (EBVs) are a central concept of EuropaBON as they provide a standardised framework for biodiversity monitoring and reporting. In 2023, EuropaBON had identified 70 EBVs (Junker et al., 2023) that are policy-relevant for the EU, and measurable with available and existing technologies and with a proven track record of feasibility in ongoing initiatives. EBVs require workflows to process the raw data (primary observations) through data integration and modelling into spatially-explicit EBV data products (Kissling et al., 2018; Schmeller et al., 2017). These workflows can be broken down into three main components (data collection and sampling, data integration, and modelling), with additional aspects of data interoperability and IT infrastructure being recognised as crucial for transnational data streams (Kissling & Lumbierres, 2023). To capture information about the EBV workflows, an online workshop was held on 22–24 February 2023 with 520 registered participants from 49 countries, covering a large range of expertise (Lumbierres & Kissling, 2023). Participants contributed information on EBV workflow components and advanced monitoring techniques, discussed initiatives, and identified tools and requirements for implementing 70 proposed EBVs. The information from the workshop participants was collected through pre-defined EBV workflow templates (provided as Google Docs). Templates were organised into rows representing the workflow components (‘Data collection and sampling’, ‘Data integration’, and ‘Modelling’) and columns reflecting the levels of maturity ('Current initiatives', 'Emerging tools and projects' or 'Future needs'). Prior to the workshop, some information on existing workflows was pre-filled based on previous EuropaBON deliverables, namely an assessment of the current biodiversity monitoring gaps in the EU (Santana et al., 2023) and an assessment of current EU monitoring workflows and bottlenecks (Morán-Ordóñez et al., 2023). After the workshop, the EBV workflow templates were processed to ensure the accuracy and relevance of the information. Each listed initiative was verified to be part of an active biodiversity monitoring scheme and pertinent to the specific EBV under consideration, cross-referencing with the initiative’s websites and other data collected by the EuropaBON deliverables (Morán-Ordóñez et al., 2023; Santana et al., 2023). Moreover, we ensured correct alignment of each initiative and listed requirements and needs with the appropriate workflow components and maturity levels. The EBV workflow templates provide insights into the current biodiversity monitoring landscape in Europe and how EBV production could be operationalized at the EU level. They offer detailed information about ongoing initiatives and projects, methodologies, and technologies that can be used to generate EBVs at a continental scale. Nevertheless, it is important to note that they do not encompass an exhaustive list of all ongoing or proposed initiatives of biodiversity monitoring in all member states of the EU. It is suggested to use them as a starting point and baseline for the further development of EBVs in a European context.

This is the source code of the chemistry-transport model TM5-MP model used for the simulations presented in the revised manuscript entitled: "Description and evaluation of a detailed gas-phase chemistry scheme in the TM5-MP global chemistry transport model" authored by S. Myriokefalitakis et al.