The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org.

The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources.

In order to halt the loss of global biodiversity and considering the United Nations Decade for Ocean Conservation Agenda, increasing efforts to improve biomonitoring programs and assessment of ecosystem health are needed. Aquatic environments are among the most complex to monitor, requiring an array of tools to assess their status and to define conservation targets. Although several parameters need to be considered for a comprehensive ecological status assessment, it is important to identify easy-to-apply high-resolution monitoring methods. Shifts in fish composition and abundance are often good indicators of ecosystem health status in relation to anthropogenic activities. However, traditional monitoring methods are strictly related to the habitat under study and cannot be applied universally. This review summarizes the importance of ecological indicators for aquatic environments subjected to anthropogenic stressors, with a particular focus on fish communities and transitional water ecosystems. We describe the main characteristics of both traditional and novel methods for fish monitoring, highlighting their advantages and shortcomings in an attempt to identify simple and reliable ways for a correct evaluation of the dynamics of aquatic ecosystems.

In order to identify how research contributes to the knowledge of marine litter as a pressure on beaches, we reviewed interactions of beach fauna with this pollutant. Entanglement of pinnipeds in fishing gear, negative correlations between macroinvertebrates abundance and sediment pollution, and the presence of plastic surrounding burrows were primary evidence of beach fauna interacting with stranded litter. Ingestion represents the main body of research; microplastic uptake by invertebrates has been studied by laboratory experiments and field collections to report the presence of polymers in tissues. In the natural context, the higher the urbanization surrounding beaches and sediment pollution, the higher the concentration of microplastics in organs of bivalves. This approach currently constitutes the main research direction, but ecotoxicological assays are emerging prospects to assess the effects of exposure to microplastics. Beached macroplastics entangle and entrap invertebrates and vertebrates, and studies have reported increasing negative interactions with seals and sea turtles. Changes in nesting and feeding behavior of resident and transient organisms have been shown as typical early warning indicators of marine litter impacts. The focus on fauna–litter interactions holds terrific potential for research and citizen science projects, which finally becomes a powerful driver towards environmental awareness on sandy beaches.

We provide an overview of the World Amphipoda Database (WAD), a global species database that is part of the World Register of Marine Species (WoRMS). Launched in 2013, the database contains entries for over 10,500 accepted species names. Edited currently by 31 amphipod taxonomists, following WoRMS priorities, the WAD has at least one editor per major group. All accepted species are checked by the editors, as is the authorship available for all of the names. The higher classification is documented for every species and a type species is recorded for every genus name. This constitutes five of the 13 priorities for completion, set by WoRMS. In 2015, five LifeWatch grants were allocated for WAD activities. These included a general training workshop in 2016, together with data input for the superfamily Lysianassoidea and for a number of non-marine groups. Philanthropy grants in 2019 and 2021 covered more important gaps across the whole group. Further work remains to complete the linking of unaccepted names, original descriptions, and environmental information. Once these tasks are completed, the database will be considered complete for 8 of the 13 priorities, and efforts will continue to input new taxa annually and focus on the remaining priorities, particularly the input of type localities. We give an overview of the current status of the order Amphipoda, providing counts of the number of genera and species within each family belonging to the six suborders currently recognized.