Jupyter Notebooks – a publishing format for reproducible computational workflows

It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents

Discourse or gimmick? Digital marginalia in online scholarship

Marginalia has been studied as discourse, as historical documentation and as evidence of reader response. As many academic texts are now available electronically, it seems a natural step to incorporate the interactive, social functions of the Web 2.0. Digital marginalia in an academic publishing context has been a largely unsuccessful venture to this date, yet there are several promising developments. Tools have emerged that enable readers annotate online texts in an approximation of paper-based marginalia, with the additional affordances of two- (or many-) way discourse, digital archiving, and the ability to hide the annotations. This article reviews the contemporary practices of digital marginalia, narrowing in to focus on digital marginalia as a form of academic discourse and peer review. I analyse several case studies of digital marginalia and discourse within this context, including Nature’s trial of open peer review, Wellcome Open Research, PLOS ONE and PubPeer’s systems, as well as my own experience using open peer review with Hypothes.is in a special ‘disrupted’ issue of the Journal of Media Practice. The article examines the relative success of these initiatives, attitudes toward open peer review and concludes with some promising developments for the future of digital marginalia and discourse in academic publishing

Towards the digital preservation of DOM-node-keyed scholarly web annotations

The current generation of annotation technologies use a set of keying techniques, often based on the Document Object Model (DOM) for representing HTML content, that link an annotation to its target content. However, when the DOM structure changes, for any reason, or browser rendering engines parse the underlying source differently, annotations can be orphaned and incorrectly re-attached. This article explores the preservation strategies that are required to ensure the longevity of scholarly annotations that use such technologies. These recommendations range from the social changes needed for the perception of annotations as first-class scholarly objects through to the technological changes and infrastructures that are needed for the preservation of such objects. It concludes with a series of recommendations for changes in practice and infrastructure that work towards the digital preservation of DOM-node-keyed scholarly web annotations

A Framework for Collaborative Curation of Neuroscientific Literature

Large models of complex neuronal circuits require specifying numerous parameters, with values that often need to be extracted from the literature, a tedious and error-prone process. To help establishing shareable curated corpora of annotations, we have developed a literature curation framework comprising an annotation format, a Python API (NeuroAnnotation Toolbox; NAT), and a user-friendly graphical interface (NeuroCurator). This framework allows the systematic annotation of relevant statements and model parameters. The context of the annotated content is made explicit in a standard way by associating it with ontological terms (e.g., species, cell types, brain regions). The exact position of the annotated content within a document is specified by the starting character of the annotated text, or the number of the figure, the equation, or the table, depending on the context. Alternatively, the provenance of parameters can also be specified by bounding boxes. Parameter types are linked to curated experimental values so that they can be systematically integrated into models. We demonstrate the use of this approach by releasing a corpus describing different modeling parameters associated with thalamo-cortical circuitry. The proposed framework supports a rigorous management of large sets of parameters, solving common difficulties in their traceability. Further, it allows easier classification of literature information and more efficient and systematic integration of such information into models and analyses

Mapping Scholarly Communication Infrastructure: A Bibliographic Scan of Digital Scholarly Communication Infrastructure

This bibliography scan covers a lot of ground. In it, I have attempted to capture relevant recent literature across the whole of the digital scholarly communications infrastructure. I have used that literature to identify significant projects and then document them with descriptions and basic information. Structurally, this review has three parts. In the first, I begin with a diagram showing the way the projects reviewed fit into the research workflow; then I cover a number of topics and functional areas related to digital scholarly communication. I make no attempt to be comprehensive, especially regarding the technical literature; rather, I have tried to identify major articles and reports, particularly those addressing the library community. The second part of this review is a list of projects or programs arranged by broad functional categories. The third part lists individual projects and the organizations—both commercial and nonprofit—that support them. I have identified 206 projects. Of these, 139 are nonprofit and 67 are commercial. There are 17 organizations that support multiple projects, and six of these—Artefactual Systems, Atypon/Wiley, Clarivate Analytics, Digital Science, Elsevier, and MDPI—are commercial. The remaining 11—Center for Open Science, Collaborative Knowledge Foundation (Coko), LYRASIS/DuraSpace, Educopia Institute, Internet Archive, JISC, OCLC, OpenAIRE, Open Access Button, Our Research (formerly Impactstory), and the Public Knowledge Project—are nonprofit.Andrew W. Mellon Foundatio

Promoting and Nurturing Interactions with Open Access Books: Strategies for Publishers and Authors (1.0).:A COPIM WP6 Research and Scoping Report

This report explores how publishers and authors can promote, nurture, and facilitate interaction with openly available books. Open access (obviously) opens up scholarship, but it also offers scope to enhance interactions between books, scholars, publishers, resources, librarians, and of course readers. This might take the form of creating communities and conversations around books, of gathering comments and hyperlinks, or of enabling updating, remixing and reusing, translating, modifying, reviewing, versioning, and forking of existing books. Open access, in short can create additional value and new avenues and formats that go beyond openness, by changing how people interact with books. Research shows that making books available in open access enhances discovery and online consultation (Snijder, 2019), but the short outline above makes clear that there is still a lot to be done to stimulate, explore, and practice the full range of book interactions made possible by open access. The first part of this report provides a literature overview that identifies the opportunities that digital technologies and enhanced interactions with open access books can provide for scholarship; it outlines some of the main types of interactions around scholarship—and around and as part of open access books more in particular—that scholars are involved in; and it showcases some of the experiments within humanities book publishing with reuse and remix; finally it presents some of the main (technological and socio-cultural) inhibitions that have prevented further uptake of these practices. The second part of this report more closely explores the technical dependencies that the introduced interactions and affordances rely upon. Doing so, it outlines and showcases various open source tools, software, technologies, platforms, infrastructures, guidelines and best practices, that lend themselves to being adopted by publishers and authors (or by publishers and authors working in collaboration with each other) to facilitate interaction around their book(s). The third part of this report then summarises the findings of the previous parts and provides recommendations, guidelines, and strategies (again, both socio-cultural and technological) for publishers and authors to further open up their books and collections to community interaction and reuse. Who is this Report for? The main communities we want to reach with this report are publishers and authors/scholars (or communities of scholars), to explore how they, by experimenting and often just making simple adjustments, can start to open up and stimulate interactions around their books. Where larger (commercial) publishers often have the resources to develop tools and workflows for interaction in-house (and often proprietary), scholar-led publishers, for example, although they have been at the vanguard of more experimental forms of publishing, have indicated that they often lack expertise and familiarity with more experimental forms of publishing and with the tools available to support them (Adema and Stone, 2017). We therefore focus in this report on open source tools and openly and freely available resources and guidelines that can help small-scale and not-for-profit book publishers that cannot afford to build their own custom platforms, to stimulate engagement around books. We also show various examples throughout this report of how publishers, publishing collectives and platforms, authors, and scholarly communities already are stimulating interaction around books in interesting ways and the tools and practices they have adopted to do so. This report focuses on interactions with books and on books within the humanities and social sciences in particular. Many of the types of interaction and interactive practices we describe within this report (such as for example open peer review and data mining), are being used and adopted more commonly within the STEM fields (where their uptake is also more widely researched). The humanities (and to a lesser extent the social sciences) in general have lower adoption rates where it concerns these types of practices and also have field specific preferences (as well as prejudices) towards many of these practices, which will be taken into account and further discussed in this report. Types of Interaction As part of our research we have identified several types of scholarly interaction taking place around books. The first part of this report is structured around some of the more common kinds of interaction that open access books afford: annotations, open peer review, remix and reuse, social scholarship and networked books, and emergent practices (including versioning, forking, and human computer interactions). This report doesn’t aim to cover all forms of interaction around books but has chosen to focus on the kinds of interactions that publishers and scholars would be able to promote and recreate with relatively simple adaptations to their workflows, systems, practices, and licensing. Each of the above identified types of interaction around books will be discussed in the next section, including how we can stimulate them and what obstacles currently exist towards their more general implementation. Throughout the next part of this report we will also be providing examples from within humanities book publishing to illustrate the different kinds of interaction. --- --- --- --- --- --- The report has itself been published in an experimental way. Making use of the advanced versioning functionalities offered by PubPub, we will iteratively update this document over the remainder of the project, thus allowing us to incorporate user feedback and new technological developments. Hence, we would be really grateful for constructive feedback from the communities out there who are already experimenting with new forms of interaction. Please don’t hesitate to leave comments either on the PubPub version (account and login required), or get in touch via email at [email protected] The report is published as a PDF here on Zenodo, while a more interactive book version that is available as a PubPub book.Community-led Open Publishing Infrastructures for Monographs (COPIM) is supported by the Research England Development (RED) Fund, and Arcadia—a charitable fund of Lisbet Rausing and Peter Baldwin

Ontology-Enhanced Educational Annotation Activities

Information and communications technology and technology-enhanced learning have unquestionably transformed traditional teaching–learning processes and are positioned as key factors to promote quality education, one of the basic sustainable development goals of the 2030 agenda. Document annotation, which was traditionally carried out with pencil and paper and currently benefits from digital document annotation tools, is a representative example of this transformation. Using document annotation tools, students can enrich the documents with annotations that highlight the most relevant aspects of these documents. As the conceptual complexity of the learning domain increases, the annotation of the documents may require comprehensive domain knowledge and an expert analysis capability that students usually lack. Consequently, a proliferation of irrelevant, incorrect, and/or poorly decontextualized annotations may appear, while other relevant aspects are completely ignored by the students. The main hypothesis proposed by this paper is that the use of a guiding annotation ontology in the annotation activities is a keystone aspect to alleviate these shortcomings. Consequently, comprehension is improved, exhaustive content analysis is promoted, and meta-reflective thinking is developed. To test this hypothesis, we describe our own annotation tool, @note, which fully implements this ontology-enhanced annotation paradigm, and we provide experimental evidence about how @note can improve academic performance via a pilot study concerning critical literary annotation

Proposal for an Organic Web, The missing link between the Web and the Semantic Web, Part 1

A huge amount of information is produced in digital form. The Semantic Web stems from the realisation that dealing efficiently with this production requires getting better at interlinking digital informational resources together. Its focus is on linking data. Linking data isn't enough. We need to provide infrastructural support for linking all sorts of informational resources including resources whose understanding and fine interlinking requires domain-specific human expertise. At times when many problems scale to planetary dimensions, it is essential to scale coordination of information processing and information production, without giving up on expertise and depth of analysis, nor forcing languages and formalisms onto thinkers, decision-makers and innovators that are only suitable to some forms of intelligence. This article makes a proposal in this direction and in line with the idea of interlinking championed by the Semantic Web.Comment: Supplementary material by Guillaume Bouzige and Mathilde Noua