Easy steps towards open scholarship

Knowing how and where to share your research may still seem a daunting task given the variety of channels. Ross Mounce, Community Coordinator for Open Science at the Open Knowledge Foundation, presents the best ways to ensure discoverable access to research outputs. He highlights the metadata power of institutional repositories and other services like Zenodo. With a combination of preprint & postprint postings, it is easy to make your research freely available

The right to read is the right to mine: Text and data mining copyright exceptions introduced in the UK.

New copyright exceptions to text and data mining for non-commercial research have recently come into effect and this is welcome news for UK researchers and research, argues Ross Mounce. Here he provides a brief overview of the past issues discouraging text and data mining and the what the future holds now that these exceptions have been introduced. But despite legal barriers being removed, many technical barriers still remain. Furthermore it remains to be decided what formally constitutes ‘non-commercial’ research

Opening-up the early stages of research: new journal RIO to publish research proposals.

Research Ideas & Outcomes (RIO) is the latest scholarly journal seeking to fix the broken scientific publishing system. It has been created specifically to enable and encourage the entire research cycle to be published, including research proposals and ideas. Founding editor Ross Mounce outlines what the journal seeks to achieve and how it will speed up the publishing process by eliminating the need for an outsourced typesetting process

Ex situ conservation of plant diversity in the world’s botanic gardens

Botanic gardens conserve plant diversity ex situ and can prevent extinction through integrated conservation action. Here we quantify how that diversity is conserved in ex situ collections across the world’s botanic gardens. We reveal that botanic gardens manage at least 105,634 species, equating to 30% of all plant species diversity, and conserve over 41% of known threatened species. However, we also reveal that botanic gardens are disproportionately temperate, with 93% of species held in the Northern Hemisphere. Consequently, an estimated 76% of species absent from living collections are tropical in origin. Furthermore, phylogenetic bias ensures that over 50% of vascular genera, but barely 5% of non-vascular genera, are conserved ex situ. While botanic gardens are discernibly responding to the threat of species extinction, just 10% of network capacity is devoted to threatened species. We conclude that botanic gardens play a fundamental role in plant conservation, but identify actions to enhance future conservation of biodiversity.We acknowledge the Cambridge University Botanic Garden and the National Environmental Research Council for financial support to S.B

A machine-compiled microbial supertree from figure-mining thousands of papers

There is a huge diversity of microbial taxa, the majority of which have yet to be fully characterized or described. Plant, animal and fungal taxa are formally named and described in numerous vehicles. For prokaryotes, by constrast, all new validly described taxa appear in just one repository: the International Journal of Systematics and Evolutionary Microbiology (IJSEM). This is the official journal of record for bacterial names of the International Committee on Systematics of Prokaryotes (ICSP) of the International Union of Microbiological Societies (IUMS). It also covers the systematics of yeasts. This makes IJSEM an excellent candidate against which to test systems for the automated and semi-automated synthesis of published phylogenies. In this paper we apply computer vision techniques to automatically convert phylogenetic tree figure images from IJSEM back into re-usable, computable, phylogenetic data in the form of Newick strings and NEXML. Furthermore, we go on to use the extracted phylogenetic data to compute a formal phylogenetic MRP supertree synthesis, and we compare this to previous hypotheses of taxon relationships given by NCBI's standard taxonomy tree. This is the world's first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Additionally we reflect on how recent changes to UK copyright law have enabled this project to go ahead without requiring permission from copyright holders, and the related challenges and limitations of doing research on copyright-restricted material

Phylogenetic position of <em>Diania</em> challenged

Liu et al.1 describe a new and remarkable fossil, Diania cactiformis. This animal apparently combined the soft trunk of lobopodians (a group including the extant velvet worms in addition to many Palaeozoic genera) with the jointed limbs that typify arthropods. They go on to promote Diania as the immediate sister group to the arthropods, and conjecture that sclerotized and jointed limbs may therefore have evolved before articulated trunk tergites in the immediate arthropod stem. The data published by Liu et al.1 do not un-ambiguously support these conclusions; rather, we believe that Diania probably belongs within an unresolved clade or paraphyletic grade of lobopodians

Publishing re-usable phylogenetic trees, in theory and practice

Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&#x27;data&#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &#xd;&#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript publication. Yet, most published trees are not archived, and there is no community standard governing the recommended format or content to ensure a re-usable phylogenetic record. Without a shift in emphasis toward re-usability, along with technology and standards to support such a shift, the value of trees (whether disseminated via public archives, or by other means) will be limited. Interviews with actual or potential secondary consumers of phylogenetic results suggest that there is a considerable market for re-use, but that most attempts end in disappointment. Phylogenetic results available via author requests, journal web sites, archival repositories and project web sites rarely include the critical information that secondary consumers seek, such as unique identifiers for biological sources (including species sources and accession numbers), indicators of quality, and documentation of the analytical methods used to obtain the results.&#xd;&#xa;Based on the analysis presented here, we suggest that enabling effective re-use entails a commitment by the research community to several changes from current practice: 1) using globally unique identifiers (GUIDs) to reference informational and material entities; 2) developing and using technology for documenting and exchanging the metadata that facilitate re-use; and 3) supporting development and use of a minimal reporting standard that indicates what data and metadata are considered essential for a re-useable phylogenetic record. We suggest that re-use may be catalyzed most rapidly by identifying and targeting (with appropriate technology) the most promising circumstances for re-use. These might include the extraction of sub-trees from large trees (for use in reconciliation, classification, and comparative analysis); the re-use of seed alignments, sub-alignments and homologized characters; the linking of phylogenies to geographic information (for use in ecology, phylogeography and biogeography); and the construction of supertrees and supermatrices