Peter Murray-Rust’s research while affiliated with University of Cambridge and other places

Twitter is in turmoil and the scholarly community on the platform is once again starting to migrate. As with the early internet, scholarly organizations are at the forefront of developing and implementing a decentralized alternative to Twitter, Mastodon. Both historically and conceptually, this is not a new situation for the scholarly community. Historically, scholars were forced to leave social media platform FriendFeed after it was bought by Facebook in 2006. Conceptually, the problems associated with public scholarly discourse subjected to the whims of corporate owners are not unlike those of scholarly journals owned by monopolistic corporations: in both cases the perils associated with a public good in private hands are palpable. For both short form (Twitter/Mastodon) and longer form (journals) scholarly discourse, decentralized solutions exist, some of which are already enjoying some institutional support. Here we argue that scholarly organizations, in particular learned societies, are now facing a golden opportunity to rethink their hesitations towards such alternatives and support the migration of the scholarly community from Twitter to Mastodon by hosting Mastodon instances. Demonstrating that the scholarly community is capable of creating a truly public square for scholarly discourse, impervious to private takeover, might renew confidence and inspire the community to focus on analogous solutions for the remaining scholarly record—encompassing text, data and code—to safeguard all publicly owned scholarly knowledge.

Ethical aspects of research continue to gain attention, be that in the process of proposing and planning research or performing, documenting or publishing it. One of the ways in which this trend manifests itself is the increasingly common addition of ethics statements to publications in fields like biomedicine, psychology or ethnography. Such ethics statements in publications provide the reader with a window into some of the practical yet typically hidden aspects of research ethics. As more and more publications are becoming available in full text and in machine readable formats through repositories like Europe PubMed Central, we propose to mine the literature for ethics statements and to extract information about the various aspects of research ethics that they address. The more standardized these statements are, the better the mined materials can be converted into structured and queryable information that can in turn be used to inform efforts towards higher levels of standardization in research ethics. This paper sketches out the motivation for such mining and outlines some methodological approaches that could be leveraged towards this end.

Ethical aspects of research are steadily receiving more attention, from descriptions of research that is proposed to be done to the documentation of ongoing research to reports about research already performed. One of the ways in which this trend manifests itself is the increasingly common addition of ethics statements to publications in fields like biomedicine, psychology or ethnography. Such ethics statements in publications provide the reader with a window into some of the practical yet typically hidden aspects of research ethics. As more and more publications are becoming available in full text and in machine readable formats through repositories like Europe PubMed Central, we propose to mine the literature for ethics statements and to extract information about the various aspects of research ethics that they address. The more standardized these statements are, the better the mined materials can be converted into structured and queryable information that can in turn be used to inform efforts towards higher levels of standardization in research ethics. This paper sketches out the motivation for such mining and outlines some methodological approaches that could be leveraged towards this end.

Humanity is facing a set of existential challenges, including the handling of the parallel and interconnected crises of climate change and biodiversity loss. In an effort to address these challenges, international bodies like the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) have been created. These bodies are producing a series of reports that compile scientific information on specific aspects of climate and biodiversity research and discuss policy options and other social implications. So far, these reports have been provided in formats that make it hard to mobilize the knowledge encapsulated in them. Our contribution demonstrates technical workflows for achieving such mobilization by mining the reports. Development of these workflows is spearheaded by young researchers from the SemanticClimate team of interns based at the National Institute of Plant Genome Research (NIPGR) in New Delhi, India, and volunteers from all over the world. The tool chain includes methods for cleaning up the formatting, for extracting and processing raw text, tables and figures and annotating them semantically with the help of controlled vocabularies, ontologies and Wikidata. The semantic information and the mined information can then be combined in a way that iteratively improves both, eventually resulting in versions of the reports wherein entities like species, countries or references are semantically marked up and rendered in responsive formats. Our framework supports multilingual and specialist interests (e.g., endangered species, plant chemistry), and we will also briefly discuss how the use of standard open licensing could further contribute to mobilizing information from the reports. We are keen to work with other groups sharing these interests as well as with the teams involved in producing the reports.

Background 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. New information 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.

It’s tough for Peter getting out of bed today – yesterday he travelled to Brussels and back, fighting for ‘The Right to Read is the Right to Mine’ (R2RR2M). Content mining – also known as text and data mining (TDM) – is a hot topic in Europe. It’s got huge promise, with two million scholarly publications a year and so much data that we can’t take it all in – 5,000 papers a day (and grey literature, and theses, and…). So we must have machines to help.