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