Edward Baker

Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal

Driven by changes to policies of governments and funding agencies, Open Access to content and data is quickly becoming the prevailing model in academic publishing. Open Access benefits scientists with greater dissemination and citation of their work, and provides society as a whole with access to the latest research. Open Access is, however, only one facet of scholarly communication. Core scientific statements or assertions are intertwined and hidden in the scholarly narratives, and the data underlying these statements are often obscured to the point that replication of results is impossible (Nature Editorial 2012). This is in part a result of the way scientific papers are written as narratives, rather than sources of data. An often cited reason for the lack of published data is the absence of a reward mechanism for the individuals involved in creating and managing information (Smith 2009, Costello 2009, Vision 2010, McDade et al. 2011, Duke and Porter 2013). Preparing data for publication is a time consuming activity that few scholars will undertake without recognition from their peers. Data papers are a potential solution to this problem (Chavan and Penev 2011, Chavan and Penev 2013). They allow authors to publish data and receive reward through the traditional citation process. Coupling tools to rapidly and simply generate publications will incentivise this behaviour and create a culture of data curation and sharing within the biodiversity science community. If we are going to incentivise the mass publication of data, we also need mechanisms to ensure quality. Traditional peer review is one of the bottlenecks in standard publication practice (Hauser and Fehr 2007, Fox and Petchey 2010). A common criticism of peer review is the lack of transparency and accountability on the part of the reviewers. To cope with the additional volume of papers created by data publication and to move to a more transparent system, we need to rethink peer review. We need both new methods of reviewing and new tools to automate as much of the review process as possible. This requires a new publishing platform, not just a new journal. An abundance of small isolated datasets does not, however, allow us to address the fundamental problems within the biodiversity science community. These islands of data are only of value if connected and interlinked. The task of interlinking is performed by biodiversity data aggregators like the Global Biodiversity Information Facility (GBIF) and Encylopedia of Life (EOL) which form the backbone of data-driven biodiversity research. By automating the submission of data to these aggregators, we can increase their value to more than the sum of their parts, making small data big. A renewed appreciation of the value of small data will help to reduce the vast amount of research data that exists only on laptops and memory sticks - data that is often lost when people change roles or retire. Works of potentially very limited length can hold intrinsic value to the community, but are almost impossible to publish in traditional journals chasing impact factors. Examples include single species descriptions, local checklists and software descriptions, or ecological surveys and plot data. An infrastructure that allows datasets of any size to be important means we can publish them at any time. There is no need to wait for datasets to reach a critical mass suitable for publication in a traditional journal. Today, we are pleased to announce the official release of the first series of papers published in Biodiversity Data Journal (BDJ). After years of hard work in analyzing, planning and programming the Pensoft Writing Tool (PWT), we now have a publishing platform that addresses the key concerns raised above. This provides the first workflow to support the full life cycle of a manuscript - from writing through submission, community peer-review, publication and dissemination, all within a single online collaborative environment. Shortening distance between “data” and “narrative” publishing Most journals nowadays clearly separate data from narrative (text). Moreover, data publishing through data centres and repositories has almost become a separate sector within the scholarly publishing landscape. BDJ is not a conventional journal, nor is it a conventional “data journal”. It aims to integrate data and text in a single publication by converting several kinds of biodiversity data (e.g., species occurrences, checklists, or data tables) into the text for human-readable use, while simultaneously making data units from the same article harvestable and downloadable. The text itself is marked up and presented in a highly structured and machine readable form. BDJ aims to integrate small data into the text whenever possible. Supplementary data files that underpin graphs, hypotheses and results can also be uploaded on the journal’s website and published with the article. Nonetheless, this is usually not possible for large or complex data, for which we recommend deposition in an established open international repository (for details, see Penev et al. 2011): Large primary biodiversity data sets (e.g., institutional collections of species-occurrence records) should be published with the GBIF Integrated Publishing Toolkit (IPT); small data sets of this kind are imported into the article text through an Excel template, available in PWT. Genomic data should be deposited with INSDC (GenBank/EMBL/DDBJ), either directly or via a partnering repository, e.g. Barcode of Life Data Systems (BOLD). Transcriptomics data should be deposited in Gene Expression Omnibus (GEO) or ArrayExpress. Phylogenetic data should be deposited at TreeBASE, either directly or through the Dryad Data Repository. Biodiversity-related geoscience and environmental data should be deposited in PANGAEA. Morphological images other than those presented in the article should be deposited at Morphbank. Images of a specific kind should be deposited in appropriate repositories if these exist (e.g., Morphosource for MicroCT data). Videos should be uploaded to video sharing sites like YouTube, Vimeo or SciVee and linked back to the article text. Similarly, audio files should go to platforms like FreeSound or SoundCloud, and presentations to Slideshare. In addition, multimedia files can also be uploaded as supplementary files on the journal’s website. 3D and other interactive models can be embedded in the article’s HTML and PDF. Any other large data sets (e.g., ecological observations, environmental data, morphological and other data types) should be deposited in the Dryad Data Repository, either prior to or upon acceptance of the manuscript. Other specialised data repositories can be used if these offer unique identifiers and long-term preservation. All external data used in a BDJ paper must be cited in the reference list, and links to these data (as deposited in external repositories) must be included in a separate data resources section of the article. All datasets, images or multimedia are freely downloadable from the text under the Open Data Commons Attribution License or a Creative Commons CC-Zero waiver / Public Domain Dedication. The article text is available under a Creative Commons (CC-BY) 3.0 license. Primary biodiversity data within an article can be exported in Darwin Core Archive format, which makes them interoperable with biodiversity tools based on the Darwin Core standard. By facilitating open access to the data that underlie every publication, BDJ is setting a new standard in transparency and repeatability in biodiversity science. Perpetual and universal access to primary data stimulates scientific progress by helping authors build upon existing datasets. BDJ’s commitment to supporting automated data aggregation and interlinking is happening alongside multiple advances in biodiversity informatics infrastructure that herald the dawning of an era of collaborative, big-data biodiversity science (Page 2008, Patterson et al. 2010, Thessen and Patterson 2011, Parr et al. 2012).

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science.

Abstract The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project’s operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.

Open source data logger for low-cost environmental monitoring

Abstract The increasing transformation of biodiversity into a data-intensive science has seen numerous independent systems linked and aggregated into the current landscape of biodiversity informatics. This paper outlines how we can move forward with this programme, incorporating real time environmental monitoring into our methodology using low-power and low-cost computing platforms.

BioAcoustica: a free and open repository and analysis platform for bioacoustics.

We describe an online open repository and analysis platform, BioAcoustica (http://bio.acousti.ca), for recordings of wildlife sounds. Recordings can be annotated using a crowdsourced approach, allowing voice introductions and sections with extraneous noise to be removed from analyses. This system is based on the Scratchpads virtual research environment, the BioVeL portal and the Taverna workflow management tool, which allows for analysis of recordings using a grid computing service. At present the analyses include spectrograms, oscillograms and dominant frequency analysis. Further analyses can be integrated to meet the needs of specific researchers or projects. Researchers can upload and annotate their recordings to supplement traditional publication. Database URL: http://bio.acousti.ca

Linking multiple biodiversity informatics platforms with Darwin Core Archives

Abstract 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.

NightLife: A cheap, robust, LED based light trap for collecting aquatic insects in remote areas

Inland waters cover less than 1% of our planets surface, yet provide habitat to approximately one hundred thousand aquatic insect species, i.e. those with at least one aquatic lifestage (Balian et al. 2008, Dijkstra et al. 2014). Considering the taxonomic deficit in these groups this figure is likely a significant underestimate of the true aquatic insect diversity (Dijkstra et al. 2014). The majority of aquatic insect diversity is comprised of true flies (Diptera), followed by caddisflies (Trichoptera), beetles (Coleoptera), dragonflies (Odonata), stoneflies (Plecoptera) and mayflies (Ephemeroptera) (Balian et al. 2008, Dijkstra et al. 2014). The ecology of these groups has been the focus of significant study due to their role as bioindicators of water quality, as many species are sensitive to pollution and sudden changes in their environment (Rosenberg and Resh 1993). In addition many aquatic dipteran species are vectors of disease (e.g. Currie and Adler 2008, Rueda 2008). Aquatic insects are surveyed using a variety of methods including light trapping (e.g. Collier et al. 1997) which attracts emergent adults, and often mayfly subadults, using mercury vapour (MV) bulbs or actinic fluorescent tubes. Light trapping can be either active: attended light sheets, or passive: a combination of a light with a trap (Hardwick 1968, Hienton 1974). Passive traps allow samples from multiple sites to be collected in parallel by an individual in the field, with the number of sampling sites limited by the size and weight of each trap. Current Lights Mercury vapour (MV) bulbs work by passing an arc of electric current through ionised mercury vapour; as a result these bulbs require a relatively high current to maintain the arc and thus are limited to use with either mains power or a petrol / diesel powered generator. Remote areas therefore cannot be sampled without significant effort. In addition MV bulbs are excessively bright for attracting aquatic insects, and tend to draw large numbers of night flying lepidoptera and other non-target species. MV bulbs are also delicate, easily damaged in transport and liable to break if exposed to rain during operation due to thermal fracture of the glass, and their high operating temperature is a waste of power. Actinic fluorescent tubes also use mercury, but their method of operation requires a smaller current draw. While an improvement over MV bulbs, the current draw of fluorescent tubes does still require sizeable batteries if they are to be used in remote locations. For example a single 4W flourescent tube requires a 6v 12Ah battery weighing up to 2kg for an approximate 12hr run time. Fluorescent tubes are also delicate and liable to damage under field conditions. Both MV bulbs and actinic fluorescent tubes contain mercury, which if released in the field can be hazardous for the environment. An ideal aquatic insect light trap would have these properties: Be able to run from small, standard, [potentially] rechargeable batteries. Use low power light sources, at frequencies targeted for insect vision. Be robust enough for field use without special packing or travel arrangements. Be capable of autonomous operation. Light Emitting Diodes Light Emitting Diodes (LEDs) are semiconductor devices that are used in a wide range of scientific, home and commercial lighting solutions due to the following properties: low power / high-efficiency (compared to incandescent / fluorescent) narrow spectral emissions (i.e. specific colours) long-life low-operating temperature durable (enclosed in a solid epoxy case rather than hollow glass) small size and weight These same properties also lend themselves to the use of LEDs in insect collection.

An online taxonomic database of the stick insect (Phasmida) egg-parasitising subfamilies Amiseginae and Loboscelidiinae (Hymenoptera: Chrysididae)

Abstract Background The wasp subfamilies Amiseginae and Loboscelidiinae (Hymenoptera: Chrysididae) were last catalogued in Kimsey and Bohart (1991). The subfamilies are considered to be obligate egg parasitoids of the Phasmida (stick insects), which are known to be pests in many areas of the world (Baker 2015). Our lack of knowledge of these wasps, in particular their host associations and host specificity, prevents studies into using them as potential control agents for pest phasmids. Phasmids are popular throughout the world with people from a wide range of backgrounds, from pet keepers to professional entomologists. New information A taxonomic database of the subfamilies Amiseginae and Loboscelidiinae has been created as the Chrysididae SpeciesFile, summarising the current state of scientific knowledge about these groups. In addition, a bibliography of works on these subfamilies has been created. In total information is provided for 187 valid species.

Natural History Museum Sound Archive I: Orthoptera: Gryllotalpidae Leach, 1815, including 3D scans of burrow casts of Gryllotalpa gryllotalpa (Linnaeus, 1758) and Gryllotalpa vineae Bennet-Clark, 1970.

Abstract Background The Natural History Museum (NHM) sound archive contains recordings of Gryllotalpidae, and the NHM collection holds plaster casts of the burrows of two species. These recordings and burrows have until now not been made available through the NHMs collection database, making it hard for researchers to make use of these resources. New information Eighteen recordings of mole crickets (three identified species) held by the NHM have been made available under open licenses via BioAcoustica. 3D scans of the burrows of Gryllotalpa gryllotalpa (Linnaeus, 1758) and Gryllotalpa vineae Bennet-Clark, 1970 have been made available via the NHM Data Portal.

The worldwide status of phasmids (Insecta: Phasmida) as pests of agriculture and forestry, with a generalised theory of phasmid outbreaks

Stick insects have been reported as significant phytophagous pests of agricultural and timber crops since the 1880s in North America, China, Australia and Pacific Islands. Much of the early literature comes from practical journals for farmers, and even twentieth Century reports can be problematic to locate. Unlike the plaguing Orthoptera, there has been no synthesis of the pest status of this enigmatic order of insects. This paper provides a literature synthesis of those species known to cause infestation or that are known to damage plants of economic importance; summarises historical and modern techniques for infestation management; and lists known organisms with potential for use as biological control agents. A generalised theory of outbreaks is presented and suggestions for future research efforts are made.

Global Cicada Sound Collection I: Recordings from South Africa and Malawi by B. W. Price & M. H. Villet and harvesting of BioAcoustica data by GBIF

Abstract Background Sound collections for singing insects provide important repositories that underpin existing research (e.g. Price et al. 2007 at http://bio.acousti.ca/node/11801; Price et al. 2010) and make bioacoustic collections available for future work, including insect communication (Ordish 1992), systematics (e.g. David et al. 2003), and automated identification (Bennett et al. 2015). The BioAcoustica platform (Baker et al. 2015) is both a repository and analysis platform for bioacoustic collections: allowing collections to be available in perpetuity, and also facilitating complex analyses using the BioVeL cloud infrastructure (Vicario et al. 2011). The Global Cicada Sound Collection is a project to make recordings of the worlds cicadas (Hemiptera: Cicadidae) available using open licences to maximise their potential for study and reuse. This first component of the Global Cicada Sound Collection comprises recordings made between 2006 and 2008 of Cicadidae in South Africa and Malawi. New information This collection of sounds includes 219 recordings of 133 voucher specimens, comprising 42 taxa (25 identified to species, all identified to genus) from South Africa and Malawi. The recordings have been used to underpin work on the species limits of cicadas in southern Africa, including Price et al. (2007) and Price et al. (2010). The specimens are deposited in the Albany Museum, Grahamstown, South Africa (AMGS). The harvesting of acoustic data as occurrence records by GBIF has been implemented by the Scratchpads Team at the Natural History Museum, London. This link increases the value of individual recordings and the BioAcoustica platform within the global infrastructure of biodiversity informatics by making specimen/occurence records from BioAcoustica available to a wider audience, and allowing their integration with other occurence datasets that also contribute to GBIF.