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Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren. Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C. jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloides scandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as in Chrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla and Phintelloides are redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female of Chrysilla lauta and male of C. volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from Phintella Bösenberg & Strand, 1906, Siler Simon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 and Proszynskia Kanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloides flavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloides versicolor (C. L. Koch, 1846) are redescribed. Phintelloides munita (Bösenberg & Strand, 1906) is removed from synonymy with P. versicolor. Phintella leucaspis Simon 1903 (male, Sumatra) is synonymized with P. versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.

Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication.We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-per-event observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales.

Linking records for the same taxa between different databases is an essential step when working with biodiversity data. However, name-matching alone is error-prone, because of issues such as homonyms (unrelated taxa with the same name) and synonyms (same taxon under different names). Therefore, most projects will require some curation to ensure that taxon identifiers are correctly linked. Unfortunately, formal guidance on such curation is uncommon and these steps are often ad hoc and poorly documented, which hinders transparency and reproducibility, yet the task requires specialist knowledge and cannot be easily automated without careful validation. Here, we present a case study on linking identifiers between the GBIF and NCBI taxonomies for a species checklist. This represents a common scenario: finding published sequence data (from NCBI) for species chosen by occurrence or geographical distribution (from GBIF). Wikidata, a publicly editable knowledge base of structured data, can serve as an additional information source for identifier linking. We suggest a software toolkit for taxon name-matching and data-cleaning, describe common issues encountered during curation and propose concrete steps to address them. For example, about 2.8% of the taxa in our dataset had wrong identifiers linked on Wikidata because of errors in name-matching caused by homonyms. By correcting such errors during data-cleaning, either directly (through editing Wikidata) or indirectly (by reporting errors in GBIF or NCBI), we crowdsource the curation and contribute to community resources, thereby improving the quality of downstream analyses.

Linking records for the same taxa between different databases is an essential step when working with biodiversity data. However, name-matching alone is error-prone, because of issues such as homonyms (unrelated taxa with the same name) and synonyms (same taxon under different names). Therefore, most projects will require some curation to ensure that taxon identifiers are correctly linked. Unfortunately, formal guidance on such curation is uncommon and these steps are often ad hoc and poorly documented, which hinders transparency and reproducibility, yet the task requires specialist knowledge and cannot be easily automated without careful validation. Here, we present a case study on linking identifiers between the GBIF and NCBI taxonomies for a species checklist. This represents a common scenario: finding published sequence data (from NCBI) for species chosen by occurrence or geographical distribution (from GBIF). Wikidata, a publicly editable knowledge base of structured data, can serve as an additional information source for identifier linking. We suggest a software toolkit for taxon name-matching and datacleaning, describe common issues encountered during curation and propose concrete steps to address them. For example, about 2.8% of the taxa in our dataset had wrong identifiers linked on Wikidata because of errors in name-matching caused by homonyms. By correcting such errors during data-cleaning, either directly (through editing Wikidata) or indirectly (by reporting errors in GBIF or NCBI), we crowdsource the curation and contribute to community resources, thereby improving the quality of downstream analyses. [ABSTRACT FROM AUTHOR]

Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication. We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-perevent observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales. [ABSTRACT FROM AUTHOR]

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined.

Background The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front, but differ from others by data type(s) handled, their geographic scope and the life cycle phase(s) of the data they support. In an effort to characterise the various dimensions of the biodiversity informatics landscape, we developed a framework and dataset to survey these dimensions for ten organisations (DiSSCo, GBIF, iBOL, Catalogue of Life, iNaturalist, Biodi versity Heritage Library, GeoCASe, LifeWatch, eLTER ELIXIR), relative to both their current activities and long-term strategic ambitions. New information The survey assessed the contact between the infrastructure organisations by capturing the breadth of activities for each infrastructure across five categories (data, standards, software, hardware and policy), for nine types of data (specimens, collection descriptions, opportunistic observations, systematic observations, taxonomies, traits, geological data, molecular data and literature) and for seven phases of activity (creation, aggregation, access, annotation, interlinkage, analysis and synthesis). This generated a dataset of 6,300 verified observations, which have been scored and validated by leading members of each infrastructure organisation. The resulting data allow high-level questions about the overall biodiversity informatics landscape to be addressed, including the greatest gaps and contact between organisations. [ABSTRACT FROM AUTHOR]

Background: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren., New Information: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides ; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as in Chrysilla and Siler . The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla and Phintelloides are redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female of Chrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from Phintella Bösenberg & Strand, 1906, Siler Simon, 1889 , Phintelloides Kanesharatnam & Benjamin, 2019 and Proszynskia Kanesharatnam & Benjamin, 2019 . The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species , Phintelloidesversicolor (C. L. Koch, 1846) are redescribed. Phintelloidesmunita (Bösenberg & Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized with P.versicolor .Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata., (Christa L. Deeleman-Reinhold, Wouter Addink, Jeremy A. Miller.)

Based on records dating from 1859 to 2021, we provide an overview of the marine animal diversity reported for Galiano Island, British Columbia, Canada. More than 650 taxa are represented by 20,000 species occurrence records in this curated dataset, which includes dive records documented through the Pacific Marine Life Surveys, museum voucher specimens, ecological data and crowd-sourced observations from the BC Cetacean Sightings Network and iNaturalist. [ABSTRACT FROM AUTHOR]

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined. [ABSTRACT FROM AUTHOR]

Generating regional checklists for insects is frequently based on combining data sources ranging from literature and expert assertions that merely imply the existence of an occurrence to aggregated, standard-compliant data of uniquely identified specimens. The increasing diversity of data sources also means that checklist authors are faced with new responsibilities, effectively acting as filterers to select and utilize an expert-validated subset of all available data. Authors are also faced with the technical obstacle to bring more occurrences into Darwin Core-based data aggregation, even if the corresponding specimens belong to external institutions. We illustrate these issues based on a partial update of the Kimsey et al. 2017 checklist of darkling beetles - Tenebrionidae sec. Bousquet et al. 2018 - inhabiting the Algodones Dunes of California. Our update entails 54 species-level concepts for this group and region, of which 31 concepts were found to be represented in three specimen-data aggregator portals, based on our interpretations of the aggregators' data. We reassess the distributions and biogeographic affinities of these species, focusing on taxa that are precinctive (highly geographically restricted) to the Lower Colorado River Valley in the context of recent dune formation from the Colorado River. Throughout, we apply taxonomic concept labels (taxonomic name according to source) to contextualize preferred name usages, but also show that the identification data of aggregated occurrences are very rarely well-contextualized or annotated. Doing so is a pre-requisite for publishing open, dynamic checklist versions that finely accredit incremental expert efforts spent to improve the quality of checklists and aggregated occurrence data.

The Natural History Museum, London has a number of online databases that describe interactions between species, including the HOSTS database of lepidopteran host plants (Robinson et al. 2010) and a database of Dipterocarp Seed Predators. These databases were generally bespoke software, which has increased the technical work necessary to sustain these resources. The decision was taken to migrate these to either the Scratchpads Virtual Research Environment (VRE) (Smith et al. 2011) or to the museum's Data Portal (Scott et al. 2019), depending on the complexity of the existing resource, as both are being sustained by the Informatics Group at the Natural History Museum, London. Resources that can be best represented as a single table were moved to the Data Portal, while those best represented in a relational model were transferred to Scratchpads. In addition, the Phthiraptera.info Scratchpad (Smith and Broom 2019), which already contained ecological interaction data, was migrated to the new system. [ABSTRACT FROM AUTHOR]

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data. [ABSTRACT FROM AUTHOR]

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and nongovernmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are responsible for describing and monitoring natural systems, all who depend on biodiversity data for research, policy or sustainable environmental management and all who are involved in developing biodiversity informatics solutions to register interest at https://biodiversityinformatics.org/ and to participate in the next steps to establishing a collaborative alliance. The supplementary materials include brochures in a number of languages (English, Arabic, Spanish, Basque, French, Japanese, Dutch, Portuguese, Russian, Traditional Chinese and Simplified Chinese). These summarise the need for an alliance for biodiversity knowledge and call for collaboration in its establishment. [ABSTRACT FROM AUTHOR]

Natural history collections contain estimated billions of records representing a large body of knowledge about the diversity and distribution of life on Earth. Assessments of various forms of bias within the aggregated data associated with specimens in these collections have been conducted across temporal, taxonomic, and spatial domains. Considering that these biases are the sum of biases across all contributing collections to aggregate datasets, the assessment of bias at the collection level is warranted. Interactive visualization provides a powerful tool for the assessment of these biases and insight into the historical development of natural history collections, providing context for where sources of bias may originate and developing historical narratives to clarify our understanding of our own knowledge about life on Earth. Here, I present a case study on using Sankey diagrams to illustrate the development of the entomology type collection at the Academy of Natural Sciences of Drexel University in Philadelphia, Pennsylvania with the hope that extensions of these practices among individual natural history collections are modified and adopted. [ABSTRACT FROM AUTHOR]

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. This paper provides updated information on the taxonomic composition and distribution of the Annelida - terrestrial Oligochaeta (Megadrili and Enchytraeidae), Aphanoneura and Polychaeta, recorded in Europe. Data on 18 families, 11 autochthonous and 7 allochthonous, represented in our continent by a total of 800 species, are reviewed, beginning from their distinctness, phylogenetic status, diversity and global distribution, and following with major recent developments in taxonomic and faunistic research in Europe. A rich list of relevant references is appended. The Fauna Europaea Annelida - terrestrial Oligochaeta data-set, as completed in 2004, will be updated accordingly.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Gastrotricha are a meiobenthic phylum composed of 813 species known so far (2 orders, 17 families) of free-living microinvertebrates commonly present and actively moving on and into sediments of aquatic ecosystems, 339 of which live in fresh and brackish waters. The Fauna Europaea database includes 214 species of Chaetonotida (4 families) plus a single species of Macrodasyida incertae sedis. This paper deals with the 224 European freshwater species known so far, 9 of which, all of Chaetonotida, have been described subsequently and will be included in the next database version. Basic information on their biology and ecology are summarized, and a list of selected, main references is given. As a general conclusion the gastrotrich fauna from Europe is the best known compared with that of other continents, but shows some important gaps of knowledge in Eastern and Southern regions.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. For the Mollusca-Bivalvia, data from 5 families (Margaritiferidae, Unionidae, Sphaeriidae, Cyrenidae, Dreissenidae) containing 55 species are included in this paper. European freshwater bivalves belong to the Orders Unionoida and Cardiida. All the European unionoids are included in the superfamily Unionoidea, the freshwater mussels or naiads. The European cardiids belong to the following three superfamilies: Cardioidea, Cyrenoidea and Dreissenoidea. Among the Unionoidea there are the most imperilled animal groups on the planet while the Cardioidea includes the cosmopolitan genus Pisidium, the Cyrenoidea the Asiatic clam (Corbicula fluminea) and the Dreissenoidea the famous invasive zebra mussel (Dreissena polymorpha). Basic information is summarized on their taxonomy and biology. Tabulations include a complete list of the current estimated families, genera and species.

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions.

Fauna Europaea provides a public web-service with an index of scientific names of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. For Neuropterida, data from three Insect orders (Raphidioptera, Megaloptera, Neuroptera), comprising 15 families and 397 species, are included.

Fauna Europaea provides a public web-service with an index of scientific names (including synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Coleoptera represent a huge assemblage of holometabolous insects, including as a whole more than 200 recognized families and some 400,000 described species worldwide. Basic information is summarized on their biology, ecology, economic relevance, and estimated number of undescribed species worldwide. Little less than 30,000 species are listed from Europe. The Coleoptera 2 section of the Fauna Europaea database (Archostemata, Myxophaga, Adephaga and Polyphaga excl. the series Elateriformia, Scarabaeiformia, Staphyliniformia and the superfamily Curculionoidea) encompasses 80 families (according to the previously accepted family-level systematic framework) and approximately 13,000 species. Tabulations included a complete list of the families dealt with, the number of species in each, the names of all involved specialists, and, when possible, an estimate of the gaps in terms of total number of species at an European level. A list of some recent useful references is appended. Most families included in the Coleoptera 2 Section have been updated in the most recent release of the Fauna Europaea index, or are ready to be updated as soon as the FaEu data management environment completes its migration from Zoological Museum Amsterdam to Berlin Museum für Naturkunde.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, ‘Hymenoptera - Apocrita (excluding Ichneumonoidea)’ comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding the Caucasus region). The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing taxonomic specialists throughout Europe and is a unique (standard) reference suitable for many user communities in science, government, industry, nature conservation and education. The Diptera–Brachycera is one of the 58 Fauna Europaea major taxonomic groups, and data have been compiled by a network of 55 specialists. Within the two-winged insects (Diptera), the Brachycera constitute a monophyletic group, which is generally given rank of suborder. The Brachycera may be classified into the probably paraphyletic 'lower brachyceran grade' and the monophyletic Eremoneura. The latter contains the Empidoidea, the Apystomyioidea with a single Nearctic species, and the Cyclorrhapha, which in turn is divided into the paraphyletic 'aschizan grade' and the monophyletic Schizophora. The latter is traditionally divided into the paraphyletic 'acalyptrate grade' and the monophyletic Calyptratae. Our knowledge of the European fauna of Diptera–Brachycera varies tremendously among families, from the reasonably well known hoverflies (Syrphidae) to the extremely poorly known scuttle flies (Phoridae). There has been a steady growth in our knowledge of European Diptera for the last two centuries, with no apparent slow down, but there is a shift towards a larger fraction of the new species being found among the families of the nematoceran grade (lower Diptera), which due to a larger number of small-sized species may be considered as taxonomically more challenging. Most of Europe is highly industrialised and has a high human population density, and the more fertile habitats are extensively cultivated. This has undoubtedly increased the extinction risk for numerous species of brachyceran flies, yet with the recent re-discovery of Thyreophora cynophila (Panzer), there are no known cases of extinction at a European level. However, few national Red Lists have extensive information on Diptera. For the Diptera–Brachycera, data from 96 families containing 11,751 species are included in this paper.

The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

Generating regional checklists for insects is frequently based on combining data sources ranging from literature and expert assertions that merely imply the existence of an occurrence to aggregated, standard-compliant data of uniquely identified specimens. The increasing diversity of data sources also means that checklist authors are faced with new responsibilities, effectively acting as filterers to select and utilize an expert-validated subset of all available data. Authors are also faced with the technical obstacle to bring more occurrences into Darwin Core-based data aggregation, even if the corresponding specimens belong to external institutions. We illustrate these issues based on a partial update of the Kimsey et al. 2017 checklist of darkling beetles - Tenebrionidae sec. Bousquet et al. 2018 - inhabiting the Algodones Dunes of California. Our update entails 54 species-level concepts for this group and region, of which 31 concepts were found to be represented in three specimen-data aggregator portals, based on our interpretations of the aggregators' data. We reassess the distributions and biogeographic affinities of these species, focusing on taxa that are precinctive (highly geographically restricted) to the Lower Colorado River Valley in the context of recent dune formation from the Colorado River. Throughout, we apply taxonomic concept labels (taxonomic name according to source) to contextualize preferred name usages, but also show that the identification data of aggregated occurrences are very rarely well-contextualized or annotated. Doing so is a prerequisite for publishing open, dynamic checklist versions that finely accredit incremental expert efforts spent to improve the quality of checklists and aggregated occurrence data. [ABSTRACT FROM AUTHOR]

Taxonomic literature keeps records of the planet's biodiversity and gives access to the knowledge needed for its sustainable management. Unfortunately, most of the taxonomic information is available in scientific publications in text format. The amount of publications generated is very large; therefore, to process it in order to obtain high structured texts would be complex and very expensive. Approaches like citizen science may help the process by selecting whole fragments of texts dealing with morphological descriptions; but a deeper analysis, compatible with accepted ontologies, will require specialised tools. The Biodiversity Heritage Library (BHL) estimates that there are more than 120 million pages published in over 5.4 million books since 1469, plus about 800,000 monographs and 40,000 journal titles (12,500 of these are current titles). It is necessary to develop standards and software tools to extract, integrate and publish this information into existing free and open access repositories of biodiversity knowledge to support science, education and biodiversity conservation. This document presents an algorithm based on computational linguistics techniques to extract structured information from morphological descriptions of plants written in Spanish. The developed algorithm is based on the work of Dr. Hong Cui from the University of Arizona; it uses semantic analysis, ontologies and a repository of knowledge acquired from the same descriptions. The algorithm was applied to the books Trees of Costa Rica Volume III (TCRv3), Trees of Costa Rica Volume IV (TCRv4) and to a subset of descriptions of the Manual of Plants of Costa Rica (MPCR) with very competitive results (more than 92.5% of average performance). The system receives the morphological descriptions in tabular format and generates XML documents. The XML schema allows documenting structures, characters and relations between characters and structures. Each extracted object is associated with attributes like name, value, modifiers, restrictions, ontology term id, amongst other attributes. The implemented tool is free software. It was developed using Java and integrates existing technology as FreeLing, the Plant Ontology (PO), the Plant Glossary, the Ontology Term Organizer (OTO) and the Flora Mesoamericana English-Spanish Glossary. [ABSTRACT FROM AUTHOR]

Fauna Europaea is Europe's main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea), Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts.

We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

We describe an implementation of the Darwin Core Archive (DwC-A) standard that allows for the exchange of biodiversity information contained within the Scratchpads virtual research environment with external collaborators. Using this single archive file Scratchpad users can expose taxonomies, specimen records, species descriptions and a range of other data to a variety of third-party aggregators and tools (currently Encyclopedia of Life, eMonocot Portal, CartoDB, and the Common Data Model) for secondary use. This paper describes our technical approach to dynamically building and validating Darwin Core Archives for the 600+ Scratchpad user communities, which can be used to serve the diverse data needs of all of our content partners.

The BioCASe Monitor Service (BMS) is a web-based tool for coordinators of distributed data networks that provide information to web-portals and data aggregators via the BioCASe Provider Software. Building on common standards and protocols, it has three main purposes: (1) monitoring provider’s progress in data provision, (2) facilitating checks of data mappings with a focus on the structure, plausibility and completeness, and (3) verifying compliance of provided data for transformation into other target schemas. Herein two use cases, GBIF-D and OpenUp!, are presented in which the BMS is being applied for monitoring the progress in data provision and performing quality checks on the ABCD (Access to Biological Collection Data) schema mapping. However, the BMS can potentially be used with any conceptual data schema and protocols for querying web services. Through flexible configuration options it is highly adaptable to specific requirements and needs. Thus, the BMS can be easily implemented into coordination workflows and reporting duties within other distributed data network projects.