One document, many users: what happens when you re-purpose a document?

To assess global challenges surrounding issues such as climate change and invasive species requires a baseline of historical data. We are fortunate in biodiversity that such data exists in a rich body of literature. One such source of historical data is the Biologia Centrali-Americana (BCA), which documents the plant and animal life in Central America one hundred years’ ago, and which can be compared to contemporary species distributions. This valuable resource has recently been re-keyed and manually marked up by the INOTAXA project (http://www.inotaxa.org/). The 56-volume work is now being curated before wider release. The manual annotation of the BCA is both time consuming in its initial phases and demands expert review to curate the results. This manual approach to mining historic texts is not viable for large-scale works such as the BCA. Attempts to automate the process face the problem of not having suitable corpora against which to develop and then test automated solutions such as text mining. One project, ViBRANT (http://vbrant.eu/), sought to use the scale of the re-keyed data being produced by INOTAXA to develop a solution to this problem. However, this apparently straightforward task has thrown up many issues because different audiences have different requirements of the mark up. This presentation describes the process by which the BCA is being reworked from digitisation through to a curated document corpus. The intended users are biodiversity scientists who can use the corpus for taxonomic and biodiversity research, and computer scientists who can use it to develop new text mining and mark up tools. The presentation covers the different requirements of scientists in the two domains, how this affects the mark up required of the documents, and how to re-purpose the annotations to meet the needs of different and sometimes disparate scientific audiences

From XML to XML: The why and how of making the biodiversity literature accessible to researchers

We present the ABLE document collection, which consists of a set of annotated volumes of the Bulletin of the British Museum (Natural History). These follow our work on automating the markup of scanned copies of the biodiversity literature, for the purpose of supporting working taxonomists. We consider an enhanced TEI XML markup language, which is used as an intermediate stage in translating from the initial XML obtained from Optical Character Recognition to the target taXMLit. The intermediate representation allows additional information from external sources such as a taxonomic thesaurus to be incorporated before the final translation into taXMLit

Family-group names in Coleoptera (Insecta)

We synthesize data on all known extant and fossil Coleoptera family-group names for the first time. A catalogue of 4887 family-group names (124 fossil, 4763 extant) based on 4707 distinct genera in Coleoptera is given. A total of 4492 names are available, 183 of which are permanently invalid because they are based on a preoccupied or a suppressed type genus. Names are listed in a classification framework. We recognize as valid 24 superfamilies, 211 families, 541 subfamilies, 1663 tribes and 740 subtribes. For each name, the original spelling, author, year of publication, page number, correct stem and type genus are included. The original spelling and availability of each name were checked from primary literature. A list of necessary changes due to Priority and Homonymy problems, and actions taken, is given. Current usage of names was conserved, whenever possible, to promote stability of the classification.We would like to sincerely thank the following people for their assistance with nomenclatural and/or bibliographical issues during this project: R. Aalbu (Tenebrionidae), A. Bennett (Hymenoptera), C. Chaboo (Chrysomelidae), C. Bellamy (Buprestidae), L. Bocák (various), M. Bologna (Meloidae), P. Bouchet (Gastropoda), M. Brancucci (publication dates), M. Buck (Hymenoptera), P. Cate (Elateridae), D. Chandler (Anthicidae), C. Costa (Elateridae), J. Cracraft (Aves), J. Cumming (Diptera), H. Douglas (Elateridae), M. Engel (Hymenoptera), W. Eschmeyer (Pisces), N. Evenhuis (Diptera), C. Ferraris (Pisces), G. Flores (literature), R. Foottit (Hemiptera), G. Gibson (Hymenoptera), B. Gill (Scarabaeoidea), M. Gimmel (Cyclaxyridae), V. Grebennikov (various), V. Gusarov (Staphylinidae), A. Hamilton (Hemiptera), L. Herman (Staphylinidae), M. Ivie (Tenebrionoidea), D. Iwan (Coleoptera), E. Jendek (Buprestoidea), P. Johnson (Elateridae), P. Jolivet (Chrysomelidae), S. Kazantsev (literature), I. Kitching (Lepidoptera), J. Kolibáč (Cleridae), H. Labrique (literature), D. Lafontaine (Lepidoptera), S. Laplante (various), M. LeCroy (Aves), S. Laplante (Coleoptera), A. Legalov (Curculionoidea), L. LeSage (Chrysomelidae), R. Leschen (various), I. Löbl (various), O. Lonsdale (Diptera), E. Matthews (Tenebrionidae), O. Merkl (Tenebrionidae), E. Michel (ICZN Cases), J. Muona (Eucnemidae, Elateridae), J. Nieto Nafría (Hemiptera), R. Oberprieler (Curculionoidea), J. O’Hara (Diptera), W. Opitz (Cleridae), D. Pavićević (Staphylinidae), K. Philips (Ptinidae), J. Pinto (Meloidae), G. Poinar (Curculionoidea), D. Pollock (Tenebrionoidea), R. Pyle (Pisces), D. Reeder (Mammalia), F. Riedel (Mollusca), C. Roper (Cephalopoda), C. Schmidt (Lepidoptera), N. Simmons (Mammalia), J. Skevington (Diptera), A. Smetana (various), W. Steiner (Tenebrionidae), M. Thayer (stems, Staphyliniformia), C. Thompson (Diptera), F. Vaz-de-Mello (Scarabaeidae), T. Virro (Rotifera), R. Wharton (Hymenoptera) and Q. Yu (Nematoda). M. Thayer provided data on the correct stem of Coleoptera genera. S. Gamman and P. Madaire, the library staff at Agriculture and Agri-Food Canada (Ottawa), are thanked for their assistance with acquisition of important literature. A. Newton partial grant support for catalog database construction: United States National Science Foundation grants 8814449 (Field Museum Coleoptera collection inventory), 0118749 (south temperate Staphylinidae catalog) and 0715705 (world Staphylinini catalog).Peer Reviewe

Digitising legacy zoological taxonomic literature: Processes, products and using the output

By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future

Systematics and Phylogeny of Weevils

This Special Issue on the Systematics and Phylogeny of Weevils presents 31 new research papers on one of the most diverse and successful groups of animals on Earth, the beetle superfamily Curculionoidea. It was in part inspired to commemorate the extraordinary life and scientific achievements of Guillermo (“Willy”) Kuschel (1918–2017), who shaped this field of science over the last century like no other weevil systematist. The papers in this memorial issue span weevil faunas from all over the globe, including South and Central America, Africa, Europe and the Near East, South-East Asia, New Guinea, Australia and New Zealand. They include major advances on the phylogeny and classification of the “broad-nosed” weevils (Entiminae), on the weevils associated with American cycads and on the unique extinct weevil fauna preserved in the 100-million-year-old Burmese amber, when weevils started to diversify alongside the oldest angiosperm plants. They comprise a tribute to Willy Kuschel, the proceedings of a weevil symposium held in his honor in 2016 in Orlando, Florida, 24 systematic studies (including seven phylogenetic analyses) and five other contributions on the diversity, biology, distribution, evolution and fossil history of weevils. In the papers collated in this volume, 30 new genera and 92 new species of weevils are described and a new family of extinct weevils is recognized

Sharing the benefits of taxonomic research: time to upgrade the model

Many permits for collecting biological samples have simple conditions, such as returning specimens and information. In meeting them researchers are ‘sharing benefits’ in the context of the Convention on Biological Diversity (CBD). However, the documents giving such conditions are often poorly connected to long-term research by many individuals, leading to tail-off of delivery. The conditions and the benefits shared are also often ineffective for biodiversity conservation because of inefficient linkage to environmental managers and policy priorities. A new model is needed to better manage permit conditions so that users of biological and genetic material are aware of the agreements and can deliver with minimal additional effort, and to provide better linkage to application in provider countries. Many of the informatics tools to permit this are already available. The paper will outline the elements of the model and suggest means of implementation

ABLE Corpus

A collection of biodiversity literature comprising TEI XML documents enhanced with taxonomic information. The collection consists of a total of 4,504 marked up pages, with about 1.6 million words