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Valérie de Crécy-Lagard: et al., Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward., National Science Foundation (grant MCB-2129768) to V.d.C.-L; National Institutes of Health Intramural Research Program, National Library of Medicine (Z.L.).

Over the past five years, Elsevier has focused on implementing FAIR and best practices in data management, from data preservation through reuse. In this paper we describe a series of efforts undertaken in this time to support proper data management practices. In particular, we discuss our journal data policies and their implementation, the current status and future goals for the research data management platform Mendeley Data, and clear and persistent linkages to individual data sets stored on external data repositories from corresponding published papers through partnership with Scholix. Early analysis of our data policies implementation confirms significant disparities at the subject level regarding data sharing practices, with most uptake within disciplines of Physical Sciences. Future directions at Elsevier include implementing better discoverability of linked data within an article and incorporating research data usage metrics.

We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in the enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.; We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in the enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.

Argument mining targets structures in natural language related to interpretation and persuasion which are central to scientific communication. Most scholarly discourse involves interpreting experimental evidence and attempting to persuade other scientists to adopt the same conclusions. While various argument mining studies have addressed student essays and news articles, those that target scientific discourse are still scarce. This paper surveys existing work in argument mining of scholarly discourse, and provides an overview of current models, data, tasks, and applications. We identify a number of key challenges confronting argument mining in the scientific domain, and suggest some possible solutions and future directions.

Next to keeping up with the growing literature in their own and related fields, scholars increasingly also need to rebut pseudo-science and disinformation. To address these challenges, computational work on enhancing search, summarization, and analysis of scholarly documents has flourished. However, the various strands of research on scholarly document processing remain fragmented. To reach to the broader NLP and AI/ML community, pool distributed efforts and enable shared access to published research, we held the 1st Workshop on Scholarly Document Processing at EMNLP 2020 as a virtual event. The SDP workshop consisted of a research track (including a poster session), two invited talks and three Shared Tasks (CL-SciSumm, Lay-Summ and LongSumm), geared towards easier access to scientific methods and results. Website: https://ornlcda.github.io/SDProc

We present the results of three Shared Tasks held at the Scholarly Document Processing Workshop at EMNLP2020: CL-SciSumm, LaySumm and LongSumm. We report on each of the tasks, which received 18 submissions in total, with some submissions addressing two or three of the tasks. In summary, the quality and quantity of the submissions show that there is ample interest in scholarly document summarization, and the state of the art in this domain is at a midway point between being an impossible task and one that is fully resolved.

To support superior ways of sharing scientific, medical and engineering knowledge, Elsevier has been an active participant in a plethora of research projects, multi-stakeholder communities, alliances and data standards organisations. As an example, we will discuss how Elsevier has contributed to organisations that advocate and govern the use of unique identifiers throughout the scholarly lifecycle. The shared use of unique identifiers for finding and linking to papers, authors, and institutions has been an area where Elsevier has invested in, from the beginning. After the resounding success of the Digital Object Identifier project, which lead to the foundation of CrossRef, a multi-stakeholder organisation that manages DOIs across the publishing landscape, Elsevier was one of the founders of ORCID, intended to assign unique identifiers to scientists. Further cross-stakeholder initiatives for identifying objects to improve findability were pursued through Force11, a multi-stakeholder organisation to improve scholarly communication, which Elsevier staff helped co-found. The RRID project advocates and governs the use of identifiers for key research resources (such as antibodies and model animals) and the Data Citation Principles advocate a common model of sharing, citing and attributing datasets, based on DOIs for Datasets. These principles have been brought to bear inside the open Mendeley Data platform, where unique identifiers are assigned to datasets, and even versions of datasets, so that distinct iterations of a collection of research data can be cited and found. Currently, Elsevier staff are collaborating with the University of Manchester to build a portal to generate identifiers for bioinformatics workflows, based on Manchester’s ‘Research Object’ specification. This will allow bioinformatics researchers to link their software, data inputs, outputs, and publications together in a single ‘Research Object’, which can be found, cited, and linked to publications.

As data repositories make more data openly available it becomes challenging for researchers to find what they need either from a repository or through web search engines. This study attempts to investigate data users’ requirements and the role that data repositories can play in supporting data discoverability by meeting those requirements. We collected 79 data discovery use cases (or data search scenarios), from which we derived nine functional requirements for data repositories through qualitative analysis. We then applied usability heuristic evaluation and expert review methods to identify best practices that data repositories can implement to meet each functional requirement. We propose the following ten recommendations for data repository operators to consider for improving data discoverability and user’s data search experience: 1. Provide a range of query interfaces to accommodate various data search behaviours. 2. Provide multiple access points to find data. 3. Make it easier for researchers to judge relevance, accessibility and reusability of a data collection from a search summary. 4. Make individual metadata records readable and analysable. 5. Enable sharing and downloading of bibliographic references. 6. Expose data usage statistics. 7. Strive for consistency with other repositories. 8. Identify and aggregate metadata records that describe the same data object. 9. Make metadata records easily indexed and searchable by major web search engines. 10. Follow API search standards and community adopted vocabularies for interoperability.

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility. In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled "Imagining Tomorrow's University." Workshop attendees were charged with launching a new dialog around open research – the current status, opportunities for advancement, and challenges that limit sharing. The workshop examined how the internet-enabled research world has changed, and how universities need to change to adapt commensurately, aiming to understand how universities can and should make themselves competitive and attract the best students, staff, and faculty in this new world. During the workshop, the participants re-imagined scholarship, education, and institutions for an open, networked era, to uncover new opportunities for universities to create value and serve society. They expressed the results of these deliberations as a set of 22 principles of tomorrow's university across six areas: credit and attribution, communities, outreach and engagement, education, preservation and reproducibility, and technologies. Activities that follow on from workshop results take one of three forms. First, since the workshop, a number of workshop authors have further developed and published their white papers to make their reflections and recommendations more concrete. These authors are also conducting efforts to implement these ideas, and to make changes in the university system. Second, we plan to organise a follow-up workshop that focuses on how these principles could be implemented. Third, we believe that the outcomes of this workshop support and are connected with recent theoretical work on the position and future of open knowledge institutions.

Sharing research data has the potential to make research more reproducible and efficient. Scientific research is a complex process and it is crucial that at the different stages of this process, researchers handle data in a way that will allow sharing and reuse. In this paper, we present a framework for the different steps involved in managing research data: a hierarchy of research data needs, and describe some of our own ongoing efforts to support these needs. Creating a good data ecosystem that supports each of these data needs requires collaboration between all parties that are involved in the generation, storage, retrieval and use of data: researchers, librarians, institutions, government offices, funders, and also publishers. We are actively collaborating with many other participants in the research data field, to develop a data ecosystem that enables data to be more useful, and reusable, throughout science and the humanities.

The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty. However, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three categories of certainty perceived by readers: one level of high certainty, and two levels of lower certainty that are somewhat less distinct, but nevertheless show a significant degree of inter-annotator agreement. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.

The Enabling FAIR Data project has brought together a broad spectrum of Earth, space, and environmental science leaders to ensure that data are findable, accessible, interoperable, and reusable.

We developed a two-stream, Apache Solr-based information retrieval system in response to the bioCADDIE 2016 Dataset Retrieval Challenge. One stream was based on the principle of word embeddings, the other was rooted in ontology based indexing. Despite encountering several issues in the data, the evaluation procedure and the technologies used, the system performed quite well. We provide some pointers towards future work: in particular, we suggest that more work in query expansion could benefit future biomedical search engines. Database URL: https://data.mendeley.com/datasets/zd9dxpyybg/1

Researchers are increasingly required to make research data publicly available in data repositories. Although several organisations propose criteria to recommend and evaluate the quality of data repositories, there is no consensus of what constitutes a good data repository. In this paper, we investigate, first, which data repositories are recommended by various stakeholders (publishers, funders, and community organizations) and second, which repositories are certified by a number of organisations. We then compare these two lists of repositories, and the criteria for recommendation and certification. We find that criteria used by organisations recommending and certifying repositories are similar, although the certification criteria are generally more detailed. We distill the lists of criteria into seven main categories: “Mission,” “Community/Recognition,” “Legal and Contractual Compliance,” “Access/Accessibility,” “Technical Structure/Interface,” “Retrievability” and “Preservation.” Although the criteria are similar, the lists of repositories that are recommended by the various agencies are very different. Out of all of the recommended repositories, less than 6% obtained certification. As certification is becoming more important, steps should be taken to decrease this gap between recommended and certified repositories, and ensure that certification standards become applicable, and applied, to the repositories which researchers are currently using.

This report documents the program and the outcomes of Dagstuhl Perspectives Workshop 11331 “The Future of Research Communication”. The purpose of the workshop was to bring together researchers from these different disciplines, whose core research goal is changing the formats, standards, and means by which we communicate science.

Researchers are increasingly required to make research data publicly available in data repositories. Although several organisations propose criteria to recommend and evaluate the quality of data repositories, there is no consensus of what constitutes a good data repository. In this paper, we investigate, first, which data repositories are recommended by various stakeholders (publishers, funders, and community organizations) and second, which repositories are certified by a number of organisations. We then compare these two lists of repositories, and the criteria for recommendation and certification. We find that criteria used by organisations recommending and certifying repositories are similar, although the certification criteria are generally more detailed. We distil the lists of criteria into seven main categories: “Mission”, “Community/Recognition”, “Legal and Contractual Compliance”, “Access/Accessibility”, “Technical Structure/Interface”, “Retrievability” and “Preservation”. Although the criteria are similar, the lists of repositories that are recommended by the various agencies are very different. Out of all of the recommended repositories, less than 6% obtained certification. As certification is becoming more important, steps should be taken to decrease this gap between recommended and certified repositories, and ensure that certification standards become applicable, and applied, to the repositories which researchers are currently using.

Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data. In our domain of interest (molecular biology studies of cancer signal transduction pathways), individual articles may contain as many as 30 small-scale individual experiments describing a variety of findings, upon which authors base their overall research conclusions. Our system automatically classifies discourse segments in these texts into seven categories (fact, hypothesis, problem, goal, method, result, implication) with an F-score of 0.68. These segments describe the essential building blocks of scientific discourse to (i) provide context for each experiment, (ii) report experimental details and (iii) explain the data's meaning in context. We evaluate our system on text passages from articles that were curated in molecular biology databases (the Pathway Logic Datum repository, the Molecular Interaction MINT and INTACT databases) linking individual experiments in articles to the type of assay used (coprecipitation, phosphorylation, translocation etc.). We use supervised machine learning techniques on text passages containing unambiguous references to experiments to obtain baseline F1 scores of 0.59 for MINT, 0.71 for INTACT and 0.63 for Pathway Logic. Although preliminary, these results support the notion that targeting information extraction methods to experimental results could provide accurate, automated methods for biocuration. We also suggest the need for finer-grained curation of experimental methods used when constructing molecular biology databases.